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.
The two NAS devices – elara and leda – are now up and running (see the Instruments section for more info). The total effective capacity is 24 Terabytes. However, the usable capacity is 12 Terabytes, as the two NASes were set up to mirror each other for greater data storage redundancy. Please note that the mirroring happens over the weekend, hence the storage will not be accessible over the weekend.
Contact the Facility Manager – Dr Dima Chirgadze (dyc21 at cam.ac.uk) – if you would like to use the storage.
The Users’s Frequently Asked Questions (FAQs) section has been added
Here is an example:
User’s Question: How does the ICARUS compare to the old machine, BCX3?
Answer: Firstly, here is a quick reminder what both machines are:
BCX3: Rigaku Ru-H3R generator, Osmic Blue optics, RAXIS IV++ image plate.
ICARUS: Bruker MICROSTAR generator, HELIOS MX optics and PLATINUM135 CCD.
As for the comparison, see for yourself… Here are the images of the two diffraction patterns taken from the same crystal, roughly in the same orientation, using BCX3 and ICARUS. Both diffraction patterns were displayed and saved as image files in MOSFLM.
A collection of manuals for using the ICARUS is now available.
See the Documentation section of the website for more details.
The X-ray machine will be opened for users from November 1st, 2010. To book the machine go to the electronic booking system (local access only).
The installation is almost complete. The cryogenic sample cooling device (Cobra by Oxford Cryosystems Ltd) is installed. First diffraction image of protein crystal (i.e. thaumatin) taken on October 14, 2010:
Exposure time: 1 sec, distance: 70 mm.
The new X-ray machine has started producing its first X-rays on October 12, 2010 at 21:05.
We have successfully received the delivery of our new X-ray machine on October 11, 2010. The installation is under way and the Bruker’s engineers are working hard to get the machine up in running. In the meantime, here are some pictures from the day’s event.
The Unloading (total weight 2.9 tonnes):
The Installation (Cees Baas and Frank Vredenbregt of Bruker are hard at work):