5PMY
PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 192)
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 | 71.407, 71.407, 150.800 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 29.410 - 1.290 |
R-factor | 0.1588 |
Rwork | 0.158 |
R-free | 0.17840 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 4d6r |
RMSD bond length | 0.027 |
RMSD bond angle | 2.368 |
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 | 1.310 |
High resolution limit [Å] | 1.290 | 7.070 | 1.290 |
Rmerge | 0.087 | 0.064 | 0.721 |
Rmeas | 0.091 | 0.067 | 0.805 |
Rpim | 0.026 | 0.019 | 0.351 |
Total number of observations | 1141539 | 8675 | 22241 |
Number of reflections | 98239 | ||
<I/σ(I)> | 16.6 | 45.4 | 2 |
Completeness [%] | 99.5 | 98.7 | 94.3 |
Redundancy | 11.6 | 11.9 | 4.9 |
CC(1/2) | 0.998 | 0.996 | 0.715 |
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 |