X-ray User Group Newsletter

Special Meeting

When: January 18th at 11am

Where: in BSB 1.120

What: An Introduction to Oxford Diffraction's Macromolecular Crystallography systems. Hear about the latest protein crystallography product, a compact macromolecular crystallography system, the Xcalibur PX Ultra, from Oxford Diffraction Ltd. (http://www.oxford-diffraction.com).

Who: Paul Loeffen, CEO Oxford Diffraction Ltd.

Contact: Dr. Robert O. Fox fox@xray.utmb.edu

X-ray User Group Meetings


Dec 29: Happy New Year.

Jan 26: Using PMB to automate your refinements.

Feb 23: TBA

Mar 23: TBA

Apr 27: TBA

When: January 26th at 11am

Where: in BSB 2.240

What: Using PMB to automate protein crystallography refinement. Hear about the latest updates to the PMB suite of programs, and utilities for refining your protein model structure. The latest version of PMB will be available at http://www.xray.utmb.edu/PMB . Check the web site for detailed information.

I will also discuss the results of our XENOCS optics tests. A summary of our results is available at: http://www.xray.utmb.edu/~white/XENOCS_REPORT.pdf

Who: Mark A. White

Contact: Dr. Mark A. White white@xray.utmb.edu

SCSB Crystallography News

Some editions of Acta Crystallographica are now available through the MML's Academic Search Premier service. Illiad is now providing the original Acta. Cryst. PDF files through interlibrary loan.

HKL2000 is now available for processing your data from home or your synchrotron visit.

PMB: The latest version of PMB fixes a few minor bugs in pmb_sca2cns, pmb_cns2phs, and pmb_refine. The most current version is always the default on our Crystallography Core's computers.

DIP2030: The in-house calibration software (RC.ScanIP and RC.CDcreate) was updated in December, and new calibrations determined.

MOSFLM, PHASER and CCP4-5.0.1 are now installed and operational on our Linux workstations.

Why wait two weeks? Skip the queue! The waiting list for the DIP2030 detector, equipped with the new MSC Blue confocal optics is now averaging two weeks. The SMART2K CCD detector system, which still has the older Gobel optics, is available for larger crystals (> 0.2mm) which diffract reasonably well. So don't wait, hop on the CCD, the queue is much shorter.

Recent SCSB Crystallography Publications:

Emily E. Scott, Mark A. White, You Ai He, Eric F. Johnson, C. David Stout, and James R. Halpert, Structure of mammalian cytochrome P450 2B4 complexed with 4-(4-chlorophenyl)imidazole at 1.9 A resolution: Insight into the range of P450 conformations and coordination of redox partner binding J. Biol. Chem 279, 26, 27294-301, 2004.(PDF)

D. Liu, Y. Zhao, X. Fan, Y. Sun and R. O. Fox, Expression, crystallization and preliminary crystallographic analysis of YciE, a stress protein from Escherichia coli, Acta Cryst. (2004). D60, 1888-1889, 2004

Balaban AT, Ghiviriga I, Czerwinski EW, De P, Faust R. , Simple synthesis of a weak nucleophilic base (4-ethyl-2,6-diisopropyl-3,5-dimethylpyridine) evidencing a double Janus group effect., J Org Chem. 2004 Jan 23;69(2):536-42.

D. Liu, Y. Zhao, X. Fan, Y. Sun and R. O. Fox, Escherichia coli stress protein YciF: expression, crystallization and preliminary crystallographic analysis, Acta Cryst. (2004). D60, 2389-2390, 2004

X-ray Crystallography Reading List – Jan

(Available from the MML via ILLIAD)

(See more at Acta Cryst. D)

Acta Cryst. (2004). D60, 2403-2406, SAD at home: solving the structure of oxalate decarboxylase with the anomalous signal from manganese using X-ray data collected on a home source, C. E. M. Stevenson, A. Tanner, L. Bowater, S. Bornemann and D. M. Lawson

Acta Cryst. (2004). D60, 2115-2125, Interactive electron-density map interpretation: from INTER to O, T. A. Jones

Acta Cryst. (2004). D60, 2144-2149, Using prime-and-switch phasing to reduce model bias in molecular replacement, T. C. Terwilliger

Acta Cryst. (2004). D60, 2150-2155, Practical aspects of the integration of different software in protein structure solution, V. Calderone

Acta Cryst. (2005). D61, 108-111,Going soft and SAD with manganese, P. S. Salgado, M. A. Walsh, M. R. L. Laurila, D. I. Stuart and J. M. Grimes

Acta Cryst. (2005). D61, 88-98, Protein imperfections: separating intrinsic from extrinsic variation of torsion angles, G. L. Butterfoss, J. S. Richardson and J. Hermans

Acta Cryst. (2005). D61, 80-87, Pros and cons of cryocrystallography: should we also collect a room-temperature data set?, K. V. Dunlop, R. T. Irvin and B. Hazes

Acta Cryst. (2005). D61, 60-66, An ultraviolet fluorescence-based method for identifying and distinguishing protein crystals, R. A. Judge, K. Swift and C. González

Acta Cryst. (2005). D61, 2-13, Real-space protein-model completion: an inverse-kinematics approach, H. van den Bedem, I. Lotan, J.-C. Latombe and A. M. Deacon

Crystallographic Meetings (IUCr) (ACA) (BCA)

Protein Crystallography in Drug Discovery: 17-19 Jan., 2005, SF, CA (info)

RapiData 2005 (Tutorial Course): 10-15 April., 2005, BNL, LI ,NY (info)

ACA: May 28-June 2, 2005, Orlando, Florida. (Info)

IuCr XX: 23-21 Aug. 2005, Florence, Italy. (info)


Beam Time

Ring Shutdown Until February ??, email to request time available (gcpcc_access@xray.utmb.edu)

Time begins at noon of 1st day. Radiation Safety - PX1Ring CurrentDirections, Hotels (PX1 225.578.7137) – Contacts: UTMB - CAMD

Let The SCSB Advance Your Research

The SCSB is here to facilitate your Structural Biology research.

Research Areas



  • User Training

  • Mentoring

  • Collaborations

User Training

The SCSB staff is always ready and happy to train your students, post-docs and technicians in the correct use of the SCSB Instrumentation. They will also pick-up a few helpful hints along the way also. The support of the SCSB and the assistance by the staff member(s) should be acknowledged in any publications.


If you do not have the expertise to perform certain types of research the SCSB staff or faculty may be able to mentor your graduate student or post-doc as a collaborative project. Mentoring requires a significant commitment by both the mentor and student learning a new field of research. The Mentor should be co-author on any publications resulting from the student's research project. The support of the SCSB should be acknowledged in any publications.


Please contact any SCSB researcher (PI) or Core Manager to discuss possible collaborate research projects. Of course such projects are at the discretion and time-restraints of the collaborator. The Collaborator should be an author on any publications resulting from the collaborative research project. The support of the SCSB should be acknowledged in any publications.

X-ray Group User Meetings

When: Last Wednesday of each month.

Where: BSB 2.240.

When: 11 am.

Why: To discuss all aspects of crystallography.

What: A small group meeting and informal presentation.

Who: Anyone interested in crystallography.

How: Contact Dr. Mark A. White white@xray.utmb.edu