- PDB-5idd: Comment on S. W. M. Tanley and J. R. Helliwell Structural dynamic... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 5idd
Title
Comment on S. W. M. Tanley and J. R. Helliwell Structural dynamics of cisplatin binding to histidine in a protein Struct. Dyn. 1, 034701 (2014) regarding the refinement of 4mwk, 4mwm, 4mwn and 4oxe and the method we have adopted.
Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 1.79 Å3/Da / Density % sol: 31.29 %
Crystal grow
Temperature: 293 K / Method: batch mode / pH: 4.7 Details: CRYSTALLIZATION CONDITIONS: 40MG HEWL (2.7MM) CO-CRYSTALLISED WITH 3MG CARBOPLATIN (8.1MM). 462.5 microL OF A 0.02M NAAC SOLUTION ALONG REMARK 280 WITH 462.5 microL OF A 0.5M NANO3 SOLUTION ...Details: CRYSTALLIZATION CONDITIONS: 40MG HEWL (2.7MM) CO-CRYSTALLISED WITH 3MG CARBOPLATIN (8.1MM). 462.5 microL OF A 0.02M NAAC SOLUTION ALONG REMARK 280 WITH 462.5 microL OF A 0.5M NANO3 SOLUTION WAS USED WITH 75 microL DMSO.
-
Data collection
Diffraction
Mean temperature: 200 K
Diffraction source
Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
Detector
Type: APEX II CCD / Detector: CCD / Date: Nov 18, 2012 / Details: CONFOCAL MIRROR OPTICS
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Resolution: 1.13→32.21 Å / Num. obs: 35817 / % possible obs: 94.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.2
Reflection shell
Resolution: 1.13→1.16 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2 / % possible all: 77
-
Processing
Software
Name
Version
Classification
REFMAC
5.7.0032
refinement
SAINT
datareduction
APEX 2
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4oxe
Resolution: 1.13→32.21 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.585 / SU ML: 0.034 / SU R Cruickshank DPI: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.047 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21982
1762
5 %
RANDOM
Rwork
0.1775
-
-
-
obs
0.17964
33282
94.09 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å