5PJX
PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 82)
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 | 71.463, 71.463, 150.381 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 29.410 - 1.350 |
R-factor | 0.1567 |
Rwork | 0.156 |
R-free | 0.17750 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 4d6r |
RMSD bond length | 0.027 |
RMSD bond angle | 2.392 |
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] | 29.410 | 29.410 | 1.370 |
High resolution limit [Å] | 1.350 | 7.270 | 1.350 |
Rmerge | 0.056 | 0.039 | 0.741 |
Rmeas | 0.058 | 0.041 | 0.817 |
Rpim | 0.017 | 0.013 | 0.338 |
Total number of observations | 1022902 | 7226 | 23664 |
Number of reflections | 86177 | ||
<I/σ(I)> | 24.8 | 69.2 | 2.2 |
Completeness [%] | 99.9 | 98.6 | 97.3 |
Redundancy | 11.9 | 10.8 | 5.6 |
CC(1/2) | 0.999 | 0.989 | 0.744 |
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 |