5PNK
PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 214)
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 | 71.421, 71.421, 150.734 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 29.410 - 1.270 |
R-factor | 0.1624 |
Rwork | 0.162 |
R-free | 0.17930 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 4d6r |
RMSD bond length | 0.027 |
RMSD bond angle | 2.371 |
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 | 1.290 |
High resolution limit [Å] | 1.270 | 6.950 | 1.270 |
Rmerge | 0.094 | 0.074 | 0.642 |
Rmeas | 0.098 | 0.078 | 0.735 |
Rpim | 0.028 | 0.022 | 0.348 |
Total number of observations | 1130727 | 9185 | 16389 |
Number of reflections | 101609 | ||
<I/σ(I)> | 14.9 | 36.1 | 1.9 |
Completeness [%] | 98.3 | 98.8 | 84.4 |
Redundancy | 11.1 | 12.1 | 3.9 |
CC(1/2) | 0.998 | 0.995 | 0.666 |
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 |