The RockMaker and RockMakerWeb have been updated to version 3.2. The major change is new GUI. The in-house Rock Imager user manual has been updated to reflect the changes, see Manuals section for more information. Access to older version of RockMakerWeb is still available, see the “Quick Links” section for the corresponding link.
The Rock Imager (by Formulatrix, Inc) has been upgraded to its maximum capacity of 1000 plates. The controlling computer has been replaced with a more powerful one running Windows 7. The in-house Formulatrix user manual has been updated to reflect the changes in the procedures and new features (see Manuals section for more information).
The sample changer BruNo2 (by Bruker AXS Ltd) has been installed on ICARUS. The sample changer is compatible with the Uni-Pucks and can accept 5 pucks at a time, i.e. 80 samples. The sample changer is capable of screening crystals or performing X-ray diffraction data collection runs in completely automated manner without user intervention.
It is located in room 1-60. Users who wish to use the sample changer must book it using our Electronic Booking System. The training will be provided by Dr Dima Chirgadze.
The Crystallographic X-ray Facility has now taken under its care and support the Oryx6 crystallisation robot by Douglas Instruments Ltd. It is an Automatic Protein Crystallisation system for protein crystallisation and can be used for performing sitting drop crystallisation, ”MMS”Microseed Matrix Screening, 2D optimisation, additive experiments, microbatch-under-oil and multi-variate optimisation.
It is located in room 1-56. Users who wish to use Oryx6 must book it using our Electronic Booking System.
To all users of the Crystallographic X-ray Facility:
The Crystallographic X-ray Facility can now offer a variety of pre-dispensed into 96-wells plates Crystallisation Screens (see the Resources section of the CXF website for the complete and up-to-date list of kits, as well as the availability of stocks).
The Screens are pre-dispensed into 96-wells, 2-drops, MRC-type plates and are in 1-12 format (compatible with Formulatrix Imager/Hotel software).
The cost is only £8.10 per plate (this includes the UV-transparent seal). Please note the price does not include the cost of plates disposal.
The list of currently available Crystallisation Screens:
see the Resources section of the CXF website for the complete and up-to-date list of kits.
If you would like to use this service, please contact Dr Dima Chirgadze (dyc21 at cam.ac.uk) or Mr Simon Quick (sq204 at cam.ac.uk).
The old equipment in the room 1.81 has finally been decommissioned (R.I.P. BCX3). This room will become the Facility’s Crystallisation Robotics Room, and its refurbishment is well under way. The new equipment, i.e. the crystallisation imager (RockImager 500), will be installed on or around March 28, 2011.
Here is a small report highlighting the statistics for the usage of ICARUS and for the X-ray diffraction data collected for the period from 1 November, 2010 to 28 February, 2011.
During this period we had no breakdowns and only had 2 days of maintenance by Bruker engineers (post-installation checks). The ICARUS is still running on its first filament from the time of installation back in October 13, 2010. Since then, the MICROSTAR generator has run at full power (45kV, 60mA) for 80% of the time. The Cobra Cryostream has been running 24/7 since it was turned on October 15, 2010.
The total number of ICARUS operational days for the period from 1 November, 2010 to 28 February, 2011 is 63 days (weekends, holiday and training closures are excluded). There are now 32 users of the Facility that are trained in the usage of ICARUS.
In terms of the X-ray data acquisition, the users have collected 108 complete datasets that resulted in protein structures. The resolution of the datasets ranged between 1.4 and 3.6 Angstrom, and dataset collection time between 10 minutes and 3 days (please note that none of those datasets included data from lysozyme or thaumatin crystals). We also estimate that about 1000 crystals were tested by users for diffraction during this period. The samples from external users run on ICARUS included amyloid fibrils and carbon nano-tubes.
About 95% of all collected datasets were processed (indexed, integrated, scaled and space group determined) using the PROTEUM2 software (Bruker AXS). The users, including novices and experts alike, are generally pleased with the supplied data processing software, commenting on its ease of use during the setup of data collection experiments as well as during the data processing calculations.
Protein structure of NK1 fragment of HGF/SF (Hepatocyte Growth Factor/Scatter Factor, PDB-ID codes: 1nk1, 1bht) has been successfully determined using Sulphur SAD (S-SAD) experiments on the in-house Cu Kalpha source (i.e. ICARUS). The protein has molecular weight of about 25 kDa and contains 12 sulphur atoms (Met and Cys). The crystals belong to P21 spacegroup and the asymmetric contains a dimer of NK1.
The S-SAD data collection was performed on ICARUS (X8 PROTEUM X-ray diffraction system). The NK1 crystal diffracted to about 2.0 Angstrom resolution (<I/sigma> in the high resolution shell is 3.5). A total of 6,079 diffraction images were recorded which took 2 days and 12 hours to acquire. The dataset’s overall redundancy is 46.
The search for the sulphur atoms as well as phasing and electron density modifications were performed using PHENIX (v1.7-650). The anomalous signal was of reasonable strength only up to 3.5 Angstrom resolution. The positions of 13 sulphur atoms (out of 24 possible) were identified, resulting in a set of phases with the figure of merit (FOM) of 0.41.
Here are the density modified S-SAD maps:
The autobuilding procedure by PHENIX using all data to 2.0 Angstrom resolution built 90% of the structure resulting in Rcryst of 23 % and Rfree of 28%.
Here is a sample of final 2Fo-Fc electron density maps:
It is indeed possible to solve protein crystal structure via Sulphur SAD using Cu Kalpha source. However, as the anomalous signal of sulphur is extremely small (delta f’’ is only 0.5 e- at Cu Kalpha), great care should be taken during the data collection, i.e. the overall dataset redundancy should be more than 30 and the crystal must survive for the duration of the data collection experiment.
The work has been performed by Dr Dima Chirgadze and Ms Anna Sigurdardottir.
The Windows XP computer that controls the data collection has been replaced with an upgraded PC running Linux OpenSuse 11.3.
Please note that the OpenSuse 11.3 is not supported by Bruker. Nevertheless, the PROTEUM2 software was thoroughly tested by the Facility staff in the OpenSuse 11.3 environment and it woks as expected.
Good news for all our Ubuntu users. Bruker’s Proteum2 diffraction data processing software can now be installed and run successfully under Ubuntu v10.04. The install is not supported by Bruker, so use it at your own risk.
The installation is not for the faint-hearted hence no “howto” is provided. Contact the Facility Manager – Dr Dima Chirgadze (dyc21 at cam.ac.uk) – if you would like to have the Proteum2 software installed on your Ubuntu system.