5PMK
PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 178)
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 | 71.563, 71.563, 150.544 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 29.450 - 1.440 |
R-factor | 0.1574 |
Rwork | 0.156 |
R-free | 0.18180 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 4d6r |
RMSD bond length | 0.025 |
RMSD bond angle | 2.323 |
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] | 29.450 | 29.450 | 1.460 |
High resolution limit [Å] | 1.440 | 7.750 | 1.440 |
Rmerge | 0.055 | 0.035 | 0.801 |
Rmeas | 0.057 | 0.036 | 0.835 |
Rpim | 0.016 | 0.010 | 0.233 |
Total number of observations | 927170 | 6603 | 42412 |
Number of reflections | 71662 | ||
<I/σ(I)> | 28 | 80.5 | 3.4 |
Completeness [%] | 99.8 | 98.3 | 97.3 |
Redundancy | 12.9 | 11.7 | 12 |
CC(1/2) | 0.999 | 0.999 | 0.860 |
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 |