oxford diffraction Xcalibur Series User manual

User Manual
Xcalibur
Single Crystal Diffractometers
February 26, 2004
Version 1.5
Oxford Diffraction Limited
68 Milton Park, Oxford, Oxfordshire.
OX14 4RX. UK
Tel: [phone]
Fax: [phone]
http://www.oxford-diffraction.com

Xcalibur Xcalibur_Manual_v1.5 Version 1.4
USER MANUAL Page ii
Important Information
This user manual applies to the Xcalibur systems manufactured in Poland by Oxford Diffraction.
Product: XCALIBUR2, XCALIBUR 3, XCALIBUR PX and XCALIBUR PX ULTRA
Model Type: CCD
Electrical Ratings: 1/N AC 230 V 50/60 Hz 4200 Watts
Before attempting to operate the system, PLEASE READ THE
INSTRUCTIONS.
This product should only be used by persons legally permitted to do so.
If the equipment is used in a manner not specified in the User Manual, the protection provided by
the equipment may be impaired.
Important Health and Safety Notice
When returning components for service or repair it is essential that the item is shipped together with
a signed declaration that the product has not been exposed to any hazardous contamination or that
appropriate decontamination procedures have been carried out so that the product is safe to
handle.
Care has been taken to ensure the information in this manual is accurate and at an appropriate
level. Please inform Oxford Diffraction if you have any suggestions for corrections or improvements
to this manual.
Xcalibur service and support is available for technical and operational issues as indicated below.
•E-mail: [email protected]
•Phone: [phone] between 8 a.m. and 4.30 p.m. (UK time), Monday to Friday
•Fax: [phone]
This users' manual has been written according to standard 89/392/EEC and further modifications.
Xcalibur is a trademark of Oxford Diffraction Limited in some jurisdictions and a registered
trademark of Oxford Diffraction Limited in other jurisdictions.
Oxford Diffraction acknowledges all trademarks and registrations.
Copyright 2003 Oxford Diffraction Limited. All rights reserved. No part of this document may be
reproduced or distributed in any form, or by any means, or stored in a database or retrieval system,
without prior written permission of Oxford Diffraction.

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Contents
1. Health and Safety Information ........................................................1
1.1 General.................................................................................................................................... 1
1.2 Electrical Safety....................................................................................................................... 2
1.2.1 Potential Electrical Hazards ........................................................................................... 2
1.2.2 Recommended Precautions........................................................................................... 2
1.2.3 First Aid .......................................................................................................................... 3
1.3 Mechanical Handling Safety.................................................................................................... 3
1.4 Safe Mechanical Practice........................................................................................................ 3
1.5 Moving Parts ........................................................................................................................... 3
1.6 X-ray Radiation........................................................................................................................ 4
1.7 Extreme Temperatures............................................................................................................ 5
1.8 Vacuum ................................................................................................................................... 5
1.9 High Pressures........................................................................................................................ 5
1.10 Hazardous or Toxic Materials ...............................................................................................5
1.11 Modifications and Service ..................................................................................................... 6
2. Introduction......................................................................................7
2.1 Scope ...................................................................................................................................... 7
2.2 How To Use This Manual........................................................................................................ 7
2.3 System Overview .................................................................................................................... 7
3. Specifications...................................................................................8
3.1 Environmental Requirements..................................................................................................8
3.2 Services................................................................................................................................... 8
3.2.1 Electrical Supply............................................................................................................. 8
3.2.2 Water Cooling ................................................................................................................ 9
3.2.3 Helium Gas Supply For Enhance Ultra (where applicable) ........................................... 9
3.3 Performance Data ................................................................................................................... 9
3.3.1 X-ray Tube (Typical Operating Conditions).................................................................... 9
3.3.2 Sapphire 2 CCD Detector ............................................................................................ 10
3.3.2.1 Sapphire 2 CCD Detector Theta and Resolution ......................................... 10
3.3.3 Sapphire 3 CCD Detector ............................................................................................ 11
3.3.3.1 Sapphire 3 CCD Detector Theta and Resolution ......................................... 11
3.3.4 Onyx CCD Detector ..................................................................................................... 12
3.3.4.1 Onyx CCD Detector Theta and Resolution .................................................. 12
3.3.5 PC CCD Interface ........................................................................................................ 13
3.3.6 Four-circle Kappa Geometry X-ray Goniometer .......................................................... 13
4.4 Electrical Data ....................................................................................................................... 14
4. Technical Description....................................................................15
4.1 Overview ............................................................................................................................... 15
4.2 CCD Detector Technology .................................................................................................... 17
4.2.1 Beryllium Window......................................................................................................... 18
4.2.2 Phosphor...................................................................................................................... 18
4.2.3 Taper............................................................................................................................ 18
4.2.4 CCD.............................................................................................................................. 18
4.2.5 Readout Speed ............................................................................................................ 18
4.2.6 Binning ......................................................................................................................... 19
4.2.7 Dark Current and MPP Mode....................................................................................... 19

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4.2.8 Radiation Damage ....................................................................................................... 19
4.2.9 Full Well Depth and 18-bit Digitisation ......................................................................... 19
4.2.10 Anti-blooming ............................................................................................................. 19
4.2.11 Vacuum ...................................................................................................................... 20
4.2.12 Fast Shutter................................................................................................................ 20
4.2.13 Zingers and Cosmic Ray Events................................................................................ 20
4.3 Four-Circle Kappa Geometry Goniometer ............................................................................ 20
4.4 X-ray Generator..................................................................................................................... 21
4.5 Software ................................................................................................................................ 22
4.5.1 Directory Structure .......................................................................................................22
4.5.2 Basic Menu Philosophy................................................................................................ 23
4.6 KMW200CCD Chiller............................................................................................................. 23
4.7 KMW3000C Chiller................................................................................................................ 23
4.8 Low Temperature Option....................................................................................................... 23
4.9 Safety Features ..................................................................................................................... 23
5. Handling, Installation, Storage and Transit Information ............24
5.1 Reception and Handling........................................................................................................ 24
5.1.1 Delivery ........................................................................................................................ 24
5.1.2 Unpacking .................................................................................................................... 24
5.1.3 Mechanical Handling.................................................................................................... 25
5.1.3.1 Weights, Dimensions and Lifting Points .......................................................... 25
5.1.3.2 Boxed Weights, Dimensions and Lifting Points on
Delivery ...................................................................................................................... 26
5.2 Installation and Setting to Work ............................................................................................27
5.2.1 Preparation of Site and Services ................................................................................. 27
5.2.1.1 Environmental Requirements .......................................................................... 27
5.2.1.2 System Layout ................................................................................................. 27
5.2.1.3 Electrical Services............................................................................................ 27
5.2.1.4 Water Supply ................................................................................................... 29
5.2.1.5 Low Temperature Option ................................................................................. 29
5.2.1.6 CCD Camera Pumping .................................................................................... 29
5.2.1.7 Helijet Option ................................................................................................... 29
5.2.2 Setting to Work............................................................................................................. 30
5.2.2.1 Equipment Required ........................................................................................ 30
5.2.2.2 Personnel Required for Installation.................................................................. 30
5.2.2.3 Setting up Procedures ..................................................................................... 30
5.3 Storage ........................................................................................................................ 32
6. Operation........................................................................................33
6.1 Controls and Indicators ......................................................................................................... 33
6.2 Initial Switch on Procedure.................................................................................................... 34
6.3 X-ray Tube Warm-up Procedure........................................................................................... 36
6.4 Software ................................................................................................................................ 37
6.4.1 Software Updates......................................................................................................... 37
6.4.2 Software Installation.....................................................................................................38
6.4.2.1 MGC interface software ................................................................................... 38
6.4.2.2 CrysAlis Software............................................................................................. 39
6.4.3 Changing Machine Correction and Set-up Files .......................................................... 39
6.5 Normal Operation.................................................................................................................. 40
6.5.1 General Commands..................................................................................................... 40

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6.5.2 Changing Xcalibur Settings.......................................................................................... 42
6.5.3 Standard Diffraction Experiment .................................................................................. 46
6.5.3.1 Crystal Mounting and Alignment............................................................................... 46
6.5.3.2 Diffraction Photographs to Determine Crystal Quality .............................................. 48
6.5.3.3 Unit Cell Determination ............................................................................................. 49
6.5.3.4 Data Collection.......................................................................................................... 52
6.5.3.5 Data Processing and Reduction ............................................................................... 53
6.5.3.5.1 Orientation Matrix ......................................................................................... 53
6.5.3.5.2 Run List......................................................................................................... 54
6.5.3.5.3 Scan Width.................................................................................................... 55
6.5.3.5.4 Background Evaluation................................................................................. 55
6.5.3.5.5 Special Corrections....................................................................................... 56
6.5.3.5.6 Outlier Rejection ........................................................................................... 57
6.5.3.5.7 Output Format............................................................................................... 58
6.5.3.6 Changing the Output Format from Data Reduction .................................................. 59
6.5.3.7 Absorption Correction ............................................................................................... 60
6.5.3.8 GRAL - Space Group Determination ........................................................................ 68
6.5.3.9 Structure Solution and Refinement........................................................................... 74
6.5.4 Ewald explorer ............................................................................................................. 74
6.5.5 Dc Movie - Replay of Data Collection Movie................................................................ 80
6.5.6 Reconstruction of Precession Photographs................................................................. 81
6.5.7 Dc opti - Optimisation of Data Collection Strategy....................................................... 86
6.5.8 Indexing and Data Reduction of Incommensurate Samples........................................ 92
6.5.9 Indexing and Data Reduction of Twinned Samples..................................................... 93
6.5.10 Extracting Data from Powder Samples...................................................................... 96
6.5.11 Refining of Machine Parameter File........................................................................... 97
6.5.12 Glossary of CrysAlis Commands ............................................................................. 100
6.6 Normal Shutdown................................................................................................................ 107
6.7 Emergency Shutdown ......................................................................................................... 107
6.7.1 Emergency Shutdown Procedure .............................................................................. 107
7. Mechanical Changeover of Detectors and X-ray Sources .......108
7.1 Interchange of CCD Detectors ............................................................................................ 108
7.1.1 Installation of Sapphire 2 and Sapphire 3 CCD detectors ......................................... 108
7.1.2 Removal of Sapphire 2 and Sapphire 3 CCD detectors ............................................ 109
7.1.3 Installation of the Onyx CCD camera......................................................................... 109
7.1.4 Removal of the Onyx CCD camera............................................................................ 112
7.2 Procedure for Interchange of the Molybdenum and Copper Enhance X-ray Source ......... 113
8. Maintenance Schedules ..............................................................117
8.1 Introduction.......................................................................................................................... 117
8.2 Weekly Maintenance Schedule........................................................................................... 117
8.3 Monthly Maintenance Schedule .......................................................................................... 117
8.4 Six Monthly Maintenance Schedule .................................................................................... 118
8.5 Yearly Maintenance Schedule ............................................................................................ 118
8.6 10,000 Hours Maintenance Schedule................................................................................. 119
9. Maintenance Instructions............................................................120
9.1 Special Tools....................................................................................................................... 120
9.2 Refining the Machine Parameter File.................................................................................. 120
9.3 Changing the X-ray Tube of Enhance................................................................................. 121

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9.4 Changing the X-ray Tube of Enhance ULTRA.................................................................... 122
9.5 X-ray Beam Stop Alignment................................................................................................ 124
9.6 Changing the Collimator of Enhance .................................................................................. 125
9.7 Changing the Collimator of Enhance Ultra.......................................................................... 126
9.8 Aligning the X-ray Collimator of Enhance ........................................................................... 126
9.9 Aligning the Enhance X-ray Source .................................................................................... 126
9.10 Aligning the Enhance Ultra X-ray Source.......................................................................... 129
9.10.1 X-ray Beam Alignment of Enhance Ultra ................................................................. 129
9.10.2 Optic Alignment of Enhance Ultra............................................................................ 131
9.10.3 Collimator Alignment of Enhance Ultra.................................................................... 131
9.10.4 Aligning the beam to the centre of the goniometer – Enhance Ultra ....................... 132
9.11 Checking the Door Safety Interlocks................................................................................. 133
9.12 Checking the Emergency stop .......................................................................................... 133
9.13 Checking the X-ray Radiation Levels................................................................................ 134
9.14 CCD Detector – Pumping Out Vacuum............................................................................. 134
9.15 Dismantling Xcalibur.......................................................................................................... 136
10. Trouble Shooting .......................................................................139
11. Spares.........................................................................................142
12. Disposal Instructions ................................................................144
12.1 X-ray Tube and CCD Detector .......................................................................................... 144
12.2 Third Party Equipment....................................................................................................... 144
13. Additional Information...............................................................145
13.1 Third Party Information...................................................................................................... 145
13.2 Drawings ........................................................................................................................... 146
13.2.1 Mechanical Drawings............................................................................................... 146
OD-01-00-15-C Xcalibur Suggested Layout........................................................... 146
OD-01-00-01 System and Component Dimensions............................................... 146
13.2.2 Electrical Drawings................................................................................................... 148
14. CE Conformity notice ................................................................150
Appendices.......................................................................................151
Appendix 1 X-ray Tubes Wave Lengths.................................................................................... 151
Appendix 2 Standard Crystal Parameters................................................................................ 151
Appendix 3 Temperature Scales Conversion............................................................................ 151
Appendix 4 Maintenance Records ............................................................................................ 151
Appendix 5 Example of Local Rules for the Xcalibur System Set Up at Oxford Diffraction...... 156

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Table of Figures
Figure 4.1.1 Components of the Xcalibur system ............................................................................. 15
Figure 4.1.2 View of the diffractometer ............................................................................................. 16
Figure 4.2.1 Schematic of a fibre-optic-coupled CCD detector for x-rays......................................... 17
Figure 4.3.1 Goniometer phi, kappa, omega and theta axes............................................................ 20
Figure 4.4.1 C3K5 X-ray Generator front panel ................................................................................ 21
Figure 4.4.2 DF3 X-ray Generator front panel .................................................................................. 21
Figure 5.2.1 Xcalibur installation procedure..................................................................................... 30
Figure 6.1.1 Location of switches...................................................................................................... 34
Figure 6.5.1 Screenshot of Image selection and Zoom .................................................................... 40
Figure 6.5.2 Screenshot of CCD parameters window....................................................................... 43
Figure 6.5.3 Screenshot of CrysAlis RED showing a diffraction image with beam stop mask ......... 43
Figure 6.5.4 Screenshot of CrysAlis program options – Instrument model I..................................... 44
Figure 6.5.5 Screenshot of CrysAlis program options –beam stop settings ..................................... 44
Figure 6.5.6 Screenshot of CrysAlis program options – PH and PT size ......................................... 45
Figure 6.5.7 Screenshot of CrysAlis profile inspector window .......................................................... 46
Figure 6.5.8 Optical alignment of the crystal..................................................................................... 47
Figure 6.5.9 Rotation photograph...................................................................................................... 48
Figure 6.5.10 Screenshot of axial photograph orientation screen .................................................... 49
Figure 6.5.11 Screenshot of Edit data collection runs....................................................................... 50
Figure 6.5.12 Screenshot of Edit data collection runs....................................................................... 52
Figure 6.5.13 Screenshot of CrysAlis data reduction screen (crystal lattice).................................... 54
Figure 6.5.14 Screenshot of CrysAlis data reduction screen (run list).............................................. 54
Figure 6.5.15 Screenshot of CrysAlis data reduction screen (scan width) ....................................... 55
Figure 6.5.16 Screenshot of CrysAlis data reduction screen (background evaluation) .................... 56
Figure 6.5.17 Screenshot of CrysAlis data reduction screen (special corrections)........................... 56
Figure 6.5.18 Screenshot of CrysAlis data reduction screen (outlier rejection)................................ 58
Figure 6.5.19 Screenshot of CrysAlis data reduction screen (output format) ................................... 58
Figure 6.5.20 Screenshot of data reduction finalisation window....................................................... 59
Figure 6.5.21 Screenshot of ‘ABS – Acquisition of movie screen’ .................................................... 61
Figure 6.5.22 Screenshot of crystal movie screen............................................................................ 62
Figure 6.5.23 Screenshot of crystal movie configuration screen ...................................................... 63
Figure 6.5.24 Screenshot of crystal movie screen............................................................................ 63
Figure 6.5.25 Screenshot of crystal movie screen............................................................................ 64
Figure 6.5.26 Screenshot of crystal movie screen (crystal shape) ................................................... 65
Figure 6.5.27 Screenshot of crystal movie screen............................................................................ 65
Figure 6.5.28 Screenshot of crystal movie screen............................................................................ 67
Figure 6.5.29 Example of absorption correction ............................................................................... 67
Figure 6.5.30 Screenshot of the GRAL plug-in Settings ................................................................... 68
Figure 6.5.31 Screenshot of the GRAL plug-in Load Window on initialisation (no file loaded)......... 69
Figure 6.5.32 Screenshot of the GRAL plug-in Load Window (File loaded from DC_GAIN8.HKL).. 69
Figure 6.5.33 Screenshot of the GRAL plug-in Load Window (Reciprocal space visualiser) ........... 70
Figure 6.5.34 Screenshot of the GRAL plug-in Centring Window..................................................... 70
Figure 6.5.35 Screenshot of the GRAL plug-in Niggli Window ......................................................... 71
Figure 6.5.36 Screenshot of the GRAL plug-in Lattice Window........................................................ 71
Figure 6.5.37 Screenshot of the GRAL plug-in Centring Window (After Niggli Reduction) .............. 72
Figure 6.5.38 Screenshot of the GRAL plug-in <E2-1> Window ...................................................... 72
Figure 6.5.39 Screenshot of the GRAL plug-in Space Group Window ............................................. 73
Figure 6.5.40 Screenshot of the GRAL plug-in INS-File Window ..................................................... 73

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Figure 6.5.41 Screenshot of Ewald explorer screen ......................................................................... 75
Figure 6.5.42 Screenshot of Ewald explorer screen with vector shown ........................................... 75
Figure 6.5.43 Screenshot of dialog box displayed when exiting the Ewald explorer ........................ 76
Figure 6.5.44 Screenshot of Ewald Explorer – Drag Selection of Reflections and Marking Skip..... 76
Figure 6.5.45 Screenshot of Ewald Explorer – Skip reflections invisible .......................................... 77
Figure 6.5.46 Screenshot of Ewald Explorer – Skip Filter Intensity Menu Selected......................... 77
Figure 6.5.47 Screenshot of Ewald Explorer – Skip Filter Intensity Window (Use Intensity Filter)... 78
Figure 6.5.48 Screenshot of Ewald Explorer – Mark Invisible Skip .................................................. 78
Figure 6.5.49 Screenshot of Ewald Explorer – Mark All Invisible Peaks Skip .................................. 79
Figure 6.5.50 Screenshot of Ewald Explorer – Skip Filter Intensity Window .................................... 79
Figure 6.5.51 Screenshot of Data Collection Movie with Unit Cell Predictions Overlayed ............... 80
Figure 6.5.52 Screenshot of Unwarp Wizard – Step 1: Orientation matrix ....................................... 81
Figure 6.5.53 Screenshot of Unwarp Wizard – Step 2: Open Run List............................................. 82
Figure 6.5.54 Screenshot of Unwarp Wizard – Step 2: Run List Loaded ......................................... 82
Figure 6.5.55 Screenshot of Unwarp Wizard – Step 2: Select Output Directory .............................. 83
Figure 6.5.56 Screenshot of Unwarp Wizard – Step 3: Creation of a Layer List .............................. 83
Figure 6.5.57 Screenshot of Unwarp Wizard – Step 3: Add a Reconstruction Layer ....................... 84
Figure 6.5.58 Screenshot of Unwarp Wizard – Step 4: Background Evaluation............................... 84
Figure 6.5.59 Screenshot of Unwarp Wizard – Step 5: Data Corrections......................................... 85
Figure 6.5.60 An Example of a Reconstructed layer......................................................................... 85
Figure 6.5.61 Screenshot of Run List Optimiser ............................................................................... 87
Figure 6.5.62 Screenshot of Run List Optimiser: Crystal Properties ................................................ 88
Figure 6.5.63 Screenshot of Run List Optimiser: Optimisation Parameters ..................................... 88
Figure 6.5.64 Screenshot of Run List Optimiser: Coverage Statistics .............................................. 89
Figure 6.5.65 Screenshot of Data Reduction: Special Corrections................................................... 94
Figure 6.5.66 Screenshot of Data Reduction: Editing of Twin Overlap Fraction .............................. 94
Figure 6.5.67 Screenshot of Powder Rings and Line Profile ............................................................ 96
Figure 6.5.68 Screenshot of Powder Pattern Data Plotted via a Spreadsheet Program .................. 96
Figure 6.5.69 Screenshot of Refine Model Window.......................................................................... 97
Figure 6.5.70 Screenshot of Refine Model (Constraining all Unit Cell Lengths to be Equal) ........... 98
Figure 6.5.71 Screenshot of Refine Model (Constraining all Unit Cell Angles to 90 degrees) ......... 98
Figure 7.1.3.1 Mounting the Onyx CCD - rotated mounting rail with screw positions..................... 110
Figure 7.1.3.2 Mounting the Onyx CCD - Position of the detector as it is mounted onto the rail.... 111
Figure 7.1.3.3 Mounting the Onyx CCD - replacing the front screw ............................................... 111
Figure 7.1.3.4 Mounting the Onyx CCD - replacing the rear screw ................................................ 111
Figure 7.2.1 Location of Enhance retaining and adjustment nuts................................................... 114
Figure 9.1.1 ‘T’ tool.......................................................................................................................... 120
Figure 9.1.2 Special tool ‘1’ ............................................................................................................. 120
Figure 9.3.1 Position of the X-ray source........................................................................................ 122
Figure 9.5.1 Beam stop adjustment screws .................................................................................... 125
Figure 9.9.1 Enhance X-ray Source mounted on Xcalibur 3........................................................... 126
Figure 9.9.2 Enhance X-ray source adjustments (front view) ......................................................... 128
Figure 9.9.3 Enhance X-ray source adjustments (top view) ........................................................... 128
Figure 9.10.1 Adjustment screws of Enhance Ultra ........................................................................ 129
Figure 9.10.2 Schematic showing the rotated beam stop (dashed line shows “up” position and solid
line shows “down” position)....................................................................................................... 130
Figure 9.10.3 Image of direct X-ray Beam ...................................................................................... 130
Figure 9.10.4 Image during optical alignment of Enhance Ultra ..................................................... 131
Figure 9.14.1 View of the access plates and pump out ports of the Sapphire and Onyx CCD
detectors ................................................................................................................................... 135

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Xcalibur Dimensions........................................................................................................................ 147
KMW3000C Dimensions ................................................................................................................. 147
KMW200CCD Dimensions .............................................................................................................. 147

HEALTH AND SAFETY INFORMATION
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1. Health and Safety Information
1.1 General
In normal operation the system is designed to operate safely. All users of Xcalibur should be aware
of potential hazards which exist in and around equipment of this type and the ways of avoiding
possible injury and equipment damage which may result from inappropriate ways of working. A
description of such potential hazards and how to avoid them is given in this section.
This manual adopts the following convention:
WARNING
Indicates a potential hazard which may result in injury or death
CAUTION
Indicates a potential hazard which may result in damage to equipment
Warning symbols on the equipment are:
Protective conductor terminal
Earth (ground) terminal
CAUTION
Risk of electric shock
CAUTION
Refer to accompanying documents
WARNING
Radiation Hazard
See original manufacturers' manuals for further safety data on third party equipment supplied with
the system. A list of these is given in this manual.
WARNING
Do not take risks. You have a responsibility to ensure the safe
condition and safe operation of equipment.
WARNING
Xcalibur should only be operated and maintained by authorised
operators of the system. An authorised operator is a person who has
undergone specialist radiation training and has been trained in the
use of Xcalibur by Oxford Diffraction personnel.

HEALTH AND SAFETY INFORMATION
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1.2 Electrical Safety
In normal use the user is protected from the dangers associated with the voltage, current and power
levels used by the equipment. Only personnel qualified to work with the voltages and currents used
by this equipment should attempt to disconnect, dismantle or modify the equipment.
1.2.1 Potential Electrical Hazards
The following list is not intended as a complete guide to all the electrical hazards on the system, but
serves to illustrate the range of potential hazards that exist:
•electric shock
•electric burn
•fire of electrical origin
•electric arcing
1.2.2 Recommended Precautions
WARNINGS
All of the electrical equipment supplied as part of the system should
be provided with a protective ground. Do not remove protective
grounds as this may give rise to an electrical safety hazard. It is
vitally important that the system is properly grounded at all times.
Follow local and national electrical regulations and procedures.
Do not defeat interlocks, remove connectors, disconnect equipment,
open safety covers, dismantle or modify equipment unless you are
qualified and authorised to do so and you are fully conversant with its
operation and potential hazards, or have total assurance through your
local electrical permit to work system that the equipment has been
made safe.
Ensure that the mains supply is fused at an appropriate rating, or
fitted with a circuit breaker, and that it can be isolated locally via a
clearly labelled, clearly visible and easily accessible isolating switch.
Isolate the supply before carrying out any maintenance work.
Never switch off the CCD detector’s power supply when the
KMW200CCD is operational. To switch off the CCD detector use the
KMW200CCD’s switch.
Do not touch any unshielded wires or connectors while mains power
is supplied to the system.
Do not allow water or any other foreign objects to come into contact
with Xcalibur’s electrical components.

HEALTH AND SAFETY INFORMATION
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1.2.3 First Aid
A course in first aid to include methods of artificial respiration is recommended for those whose
work involves equipment that may produce a high voltage.
WARNING
Do not attempt to administer first aid to someone who may have
suffered electric shock until the source of the shock has been
isolated.
Mains voltages are present in the system. High voltages are used by
the X-ray tube and power supply. These can cause serious injury or
death.
Only personnel qualified to work with high voltages and currents
should perform service or maintenance work on such equipment.
1.3 Mechanical Handling Safety
WARNING
Lifting points are provided for safe handling of components and safe
handling practice must be observed to comply with local regulations.
Check that lifting points are used only for the job intended.
The system itself and some components are heavy and require
careful handling. Use safe lifting procedures for heavy items to
prevent possible strain injury.
1.4 Safe Mechanical Practice
In normal use personnel are not required to undertake mechanical work. However, servicing or
repair may necessitate access to any part of the system. Only personnel who have been trained by
Oxford Diffraction to carry out service work on this equipment should attempt to dismantle, modify
or repair the equipment.
Water connections should be made and tested in accordance with any local and national safety
regulations.
1.5 Moving Parts
There are a number of moving parts in the system which are powered by electric motors.
WARNING
Injury could result if clothing or body parts become caught in moving
mechanisms.
Keep clothing, hands and body parts away from moving mechanisms.

HEALTH AND SAFETY INFORMATION
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1.6 X-ray Radiation
WARNING
This equipment contains an X-ray tube. Ensure that safe working
practices relating to radiation are employed. Follow any local,
national or international rules and guidelines.
Intentional or reckless misuse of the X-ray generator or its safety
devices including safety interlocks and cabinet shielding can result in
serious injury or even death.
During operation, there is an acceptable level of X-ray radiation as based on the recommendations
on risk published by the International Commission of Radiological Protection (ICRP) and endorsed
by the National Radiological Protection Board (NRPB) in the UK. For use in the UK, the Ionising
Radiations’ Regulations 1999 should be adhered to. For countries outside the UK the appropriate
laws apply such as registration and inspection.
Customers should be aware of their duty of safety to their employees and visitors.
WARNINGS
To prevent injury to personnel and possible damage to the
equipment, please note the following guidelines:
1. Only authorised personnel who have received appropriate
instruction and are aware of the laboratory rules that govern the
use of this type of system should operate the system.
2. Never dismount the beam stop when the system is operational.
3. Do not operate the system without the collimator, unless
performing the beam alignment procedure.
4. Use appropriate X-ray detection equipment to perform regular
radiation checks as per any laboratory rules
Use only genuine firmware X-ray tubes, X-ray generators,
monochromators, goniometer heads and collimators, as
recommended by your Xcalibur supplier. Use of other products may
compromise the performance of the shielding and safety system, and
may invalidate your warranty.

HEALTH AND SAFETY INFORMATION
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1.7 Extreme Temperatures
WARNINGS
1. Systems fitted with the low temperature option use liquid nitrogen
and/or liquid helium as a coolant. Liquid nitrogen and liquid
helium are cryogenic liquids and can cause cold burns. Wear
gloves when handling cryogenic liquids and use eye protection.
Refer to the information supplied with the equipment for more
information.
2. During operation both the X-ray tube and the heat sink of the CCD
power supply become hot. In normal use they are located inside a
cabinet and hot parts are not accessible. During maintenance
periods, however, it may be necessary to override the interlock so
that adjustments can be made. Therefore great care must be taken
to avoid touching either the X-ray tube or the heat sink of the CCD
power supply when they are operating and for a period of 20
minutes after operation.
1.8 Vacuum
WARNING
When handling and using X-ray tubes and the CCD detector,
particular care should be taken to avoid injury caused by possible
implosion of the vacuum tube. Wear eye protection.
1.9 High Pressures
WARNING
Know the law about high pressure gas cylinders and follow it. High
pressure cylinders are often used to store gases (typically at
pressures up to 200 bar). Most countries have laws about using them.
•Chain cylinders to a fixed object or keep them in specially
designed trolleys
•Only use approved and tested high pressure fittings
Gas cylinders become dangerous projectiles if they are ruptured or the valve is knocked off. They
can break through thick walls or travel hundreds of metres (by rocket propulsion).
1.10 Hazardous or Toxic Materials
Beryllium and beryllium oxide are toxic materials. Follow appropriate handling, shipping, use,
storage and disposal procedures and regulations. Refer to BrushWellman Material Safety Data
Sheet No. M10 for further information.
WARNING
If Beryllium is exposed to fire, it may oxidise to highly toxic beryllium
oxide powder. Do not attempt to clear up the remains of any fire, but

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contact the relevant local agency stating that there is an incident
involving possible beryllium or beryllium oxide contamination.
1.11 Modifications and Service
The manufacturer will not be held responsible for the safety, reliability or performance of the
equipment unless assembly operations, extensions, re-adjustments, modifications and repairs are
carried out only by persons authorised by the manufacturer. It should be stressed that those parts of
the equipment which are interchangeable, and which are subject to deterioration during operation,
may significantly affect the safety of the equipment.

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2. Introduction
2.1 Scope
This manual applies to the Xcalibur systems designed and manufactured by Oxford Diffraction.
2.2 How To Use This Manual
This manual is aimed at operators and maintenance personnel of the Xcalibur system. Operators of
the system should be computer literate, familiar with X-ray diffraction techniques, have had training
in the use of the Xcalibur system by Oxford Diffraction staff, and have had training about radiation
safety.
This manual is intended to provide operators with a practical guide to the system and its operation.
This is intended to familiarise the user with how the system works and provide a better
understanding of the system operation.
All personnel who are likely to operate the system or who are likely to come into contact with any of
the system components should read the HEALTH AND SAFETY INFORMATION section of the
manual. This provides basic information aimed at highlighting the safety hazards associated with
the equipment.
More detailed information and instructions for component parts of the system are given in the third
party manuals supplied with the system, which are listed in this manual. These manuals should also
be read and understood before operating the system.
The purpose of this manual is to:
•explain how to operate the equipment
•explain how to interface to the equipment
•list performance characteristics of the equipment
•describe how the equipment operates
•assist with simple fault finding and maintenance
2.3 System Overview
Xcalibur systems are single crystal diffractometers that use the property of X-ray diffraction to
determine the crystal structure of materials. They are intended for use with single crystals of
chemical substances (inorganic, organic or organo-metallic), mineralogical and biological samples.
Xcalibur systems may also be used in the analysis of powder samples. Intended samples should
have a maximum unit cell dimension of 100 Angstrom in any direction for small molecule Xcalibur
diffractometers and 500 Angstrom for macromolecular Xcalibur PX systems.
Xcalibur systems may be used with crystal conditioning devices. Specifically, low and high
temperature attachments and high pressure cells. Some minor modifications may be required by
Oxford Diffraction to enable use of these devices.

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3. Specifications
3.1 Environmental Requirements
Ambient temperature during operation 18 – 28 °C
Stability of ambient temperature during
operation
±1 °C
Storage temperature >10°C
<40°C
Relative humidity <80 % non – condensing
Location Clean, dust free environment
>2m from air conditioning or heating units
Floor covering Conductive or, if carpeted, covered with electrostatic
mats
Floor strength Able to bear system weight of 450 kg
3.2 Services
3.2.1 Electrical Supply
Total power requirements 230 V ±10 %,
63 A
3-phase
Number of outlets required 2 single-phase outlet (16 A) for Xcalibur system
1 single-phase outlet (32 A) for X-ray generator
4 single-phase outlets (for temperature attachments)
Voltage fluctuation < ±10 % ( with line voltage regulator fitted if
necessary)
Location of outlets On wall behind system
Protection Circuit breaker to be fitted to all outlets

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3.2.2 Water Cooling
Min flow rate 1.8 l/min
Pressure 0.5 - 5 bar gauge
Temperature stability ±5 °C
Temperature range 10 – 20 °C
Composition Filtered, without deposits, chemically neutral and
optically clear
3.2.3 Helium Gas Supply For Enhance Ultra (where applicable)
Purity 99.99%
Regulator low pressure regulator
Minimum pressure 0.5 bar gauge
Flow rate 30 - 40 cm3/min @ ATP
3.3 Performance Data
3.3.1 X-ray Tube (Typical Operating Conditions)
Tube Voltage (kV) setting Current (mA) setting Resulting power (kW)
Cu 2.2kW tube 40 55 2.2
Mo 2kW tube 50 30 1.5
Mo 3kW tube 55 40 2.2
Ag 2kW tube 60 25 1.5
Maximum radiation dose due to scattering
radiation at outside surface of the
enclosure (door closed)
0.6 µSv/h (with Mo 3 kW tube operating at 2.2 kW)
Maximum radiation dose due to scattering
(door open, with shutter closed)
0.18 µSv/h (with Mo 3 kW tube operating at 2.2 kW)

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3.3.2 Sapphire 2 CCD Detector
Active area 90-92 mm diagonal
CCD chip 1024 x 1024 pixels, Sapphire 2 (Kodak KAF-1001E,
scientific grade {grade 1})
Pixel size on scintillator ~ 60 µm
Scintillator material Gadox (absorption > 90% Mo K α)
Fibre optic reduction ~ 2.5:1; low distortion reduction taper
Peltier cooling -45 to -50°C (four stage cooler)
Temperature stability ± 0.05ºC (micro-processorized PID)
Analogue-to-digital resolution 18 bits in single read
System gain (for Mo) ~30 e-/X-ray
System noise (so-called read noise) <6 e- RMS
Dark current <0.2 e-/pix.s
Control processor TI DSP C50
Communication 2 mono-directional fibre-optic taxi channels
Correlated double sampling (CDS) speed 2 x 37.5 kHz
Readout time (complete duty cycle
including chip readout, CDS, analogue-to-
digital conversion, transfer detector-PC,
disk storage)
3.1 s (2 x 2 binning), 14 s (1 x 1 binning)
3.3.2.1 Sapphire 2 CCD Detector Theta and Resolution
Detector to sample distance 40 mm 60 mm 80 mm
Detector position minimum -105.0° -116.0° -116.0°
Detector position maximum 110.0° 126.0° 138.0°
Maximum resolution in 2 theta 133.7° 144.0° 152.3°
Maximum resolution in d-value (Mo) 0.386 Å 0.373 Å 0.366 Å
Detector opening angle 47.4° 35.9° 23.5°

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3.3.3 Sapphire 3 CCD Detector
Active area 90 - 92 mm diagonal
CCD chip Kodak KAF4301-E
Pixel size on scintillator 31 µm
Scintillator material Gadox
Fibre optic reduction 1.3:1; low distortion reduction taper
Peltier cooling -45ºC (four stage cooler)
Temperature stability ± 0.05ºC(micro-processor PID)
Analogue-to-digital resolution True 17 bit
System noise (so-called read noise) <10 e- RMS
Dark current <0.06 e-/pix.s
Control processor MC 68322
Communication 2 mono-directional fibre-optic taxi channels
Correlated double sampling (CDS) speed 1.5 MHz
Readout time (complete duty cycle
including chip readout, CDS, analogue-to-
digital conversion, transfer detector-PC,
disk storage)
2.8 s (4 x 4 binning)
4.4 s (2 x 2 binning)
3.3.3.1 Sapphire 3 CCD Detector Theta and Resolution
Detector to sample distance 40 mm 60 mm 80 mm
Detector position minimum -90.0° -105.0° -111.0°
Detector position maximum 111.0° 127.0° 134.0°
Maximum resolution in 2 theta 135.6° 145.8° 149.0°
Maximum resolution in d-value (Mo) 0.383 Å 0.371 Å 0.368 Å
Detector opening angle 49.2° 37.7° 24.9°