[ccp4bb] Structures with pseudo-uridine?

Dear All, I solved a structure of a pseudouridylated RNA and am now starting to write it up. Except for the ribosome, I can only find one X-ray structure that contains pseudo-uridine (Arnez JG and Steitz TA, 1994, Biochemistry 33:7560-7567). I was wondering is there any X-ray structures that I

[ccp4bb] Superposition of maps from different crystal forms

Hi all, I could really use some help with the following situation: I have electron density maps of my protein in two crystal forms. The first is the apo form which is in P43212 with a = b = 88.2, c = 159.1. If I soak a substrate for this protein into these crystals, I get a second crystal form

[ccp4bb] Position available for senior scientist or postdoc

A senior scientist or postdoctoral fellow position will be available in August 2007 in the Brinen lab in the department of Cellular and Molecular Pharmacology at the University of California, San Francisco. The Brinen lab is part of the UCSF Tropical Disease Research Unit, the UCSF Macromolecular S

[ccp4bb] Post-doc offer:

A 2-years post-doc position is open in Grenoble, France (Institut de Recherches en Technologie et Sciences pour le Vivant – iRTSV, CEA), to work on: New fluorescent protein markers to study the molecular and cellular dynamics. Research project: One of the main goals in cell biology is to cha

[ccp4bb] Error with scala after combat

Hi everybody, I process data with XDS, then I use Combat to import XDS ASCII data from CORRECT in order to scale whit Scala but it doesn't work. The message error is: * Wavelength and cell extracted from Batch headers, with rms variation: * Wavelength: 1.008000 Cell: 91.71093.670 103

Re: [ccp4bb] How do CNS deal with the His NE2 atoms coordinated with Zn2+?

It seems to me you have not patched the zinc to the histidines. there are two ways to attack this problem 1.) the proper way in a topology file define a patch residue PRES hiszc bond 1NE2 2ZN END in a parameter file set restraint and distance bond NE2 ZN 100.0 1.9

Re: [ccp4bb] R and Rfree

Hi U Sam When you say "R increases and Rfree decreases or vice versa" it's important to consider which variables they are increasing/decreasing with respect to. During a given run of Refmac (or whatever) with N iterations, where you optimise a *fixed* set of atomic/group/overall parameters with

Re: [ccp4bb] R and Rfree

It is difficult at the end of refinement - the small corrections hardly affect the R values, but should make the maps look cleaner. And R values are very correlated with the tightness of your geometric restraints - maybe you are changing these slightly too? I presume you are describing small sh

Re: [ccp4bb] How do CNS deal with the His NE2 atoms coordinated with Zn2+?

Hi there. 1) ensure you have the right name/atom descriptor for zinc in CNS in your zincs.pdb for the generate script Residue name > ZN2 Atom name > ZN+2 Type > ZN+2 (you can check these by searching though the ion.top file) 2) Use refmac. I find it is easier to decode what is going wrong with r

[ccp4bb] How do CNS deal with the His NE2 atoms coordinated with Zn2+?

Help someone ask a question. * How do CNS deal with the His NE2 atoms coordinated with Zn2+? Dear all: we have a crystal structure with a Zn2+ tetrahedron coordinated by three His NE2 atoms and one water. Is the proper coordinating distance between three His NE2 atoms and Zn2+ ion is in t

[ccp4bb] scripts for denzo with Saturn92

Hi everybody, can somebody provide an example input file for denzo and scalepack, when using a Saturn92 detector and a 4-circle goniometer from Rigaku (AFC10). I have troubles to process images with denzo, which process well on the Rigaku software (basically d*trek) - thus I'm sure the culpri

[ccp4bb] Protein crystallographer position available at MDC-Berlin

Protein crystallographer The crystallography group at the Max-Delbrück Center for Molecular Medicine Berlin-Buch is recruiting a protein crystallographer at the postdoctoral level. The position is available for three years with the possibility of extension. It is open immediately; applications