5PK6
PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 91)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I03 |
Synchrotron site | Diamond |
Beamline | I03 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2012-12-15 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.97630 |
Spacegroup name | P 43 21 2 |
Unit cell lengths | 71.297, 71.297, 150.083 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 29.350 - 2.380 |
R-factor | 0.1491 |
Rwork | 0.146 |
R-free | 0.20600 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 4d6r |
RMSD bond length | 0.013 |
RMSD bond angle | 1.538 |
Data reduction software | XDS |
Data scaling software | Aimless (0.1.27) |
Phasing software | REFMAC |
Refinement software | REFMAC (5.8.0131) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 29.350 | 29.350 | 2.490 |
High resolution limit [Å] | 2.380 | 8.260 | 2.380 |
Rmerge | 0.179 | 0.037 | 0.917 |
Rmeas | 0.186 | 0.039 | 0.957 |
Rpim | 0.051 | 0.012 | 0.267 |
Total number of observations | 205225 | 4971 | 22955 |
Number of reflections | 16149 | ||
<I/σ(I)> | 15.5 | 55.2 | 3.1 |
Completeness [%] | 99.7 | 97.9 | 97.7 |
Redundancy | 12.7 | 10.7 | 12.2 |
CC(1/2) | 0.998 | 1.000 | 0.873 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 298 | 28% PEG3350 -- 0.1M HEPES pH 7.0 -- 0.25M ammonium sulfate |