5PKV
PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 116)
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 | 71.688, 71.688, 151.031 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 29.510 - 1.350 |
R-factor | 0.1544 |
Rwork | 0.153 |
R-free | 0.17400 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 4d6r |
RMSD bond length | 0.027 |
RMSD bond angle | 2.416 |
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] | 29.510 | 29.510 | 1.380 |
High resolution limit [Å] | 1.350 | 7.400 | 1.350 |
Rmerge | 0.073 | 0.041 | 0.691 |
Rmeas | 0.076 | 0.044 | 0.766 |
Rpim | 0.021 | 0.013 | 0.318 |
Total number of observations | 1020300 | 7034 | 20395 |
Number of reflections | 86435 | ||
<I/σ(I)> | 18.7 | 47.2 | 2.2 |
Completeness [%] | 99.6 | 98.5 | 91.6 |
Redundancy | 11.8 | 10.9 | 5.3 |
CC(1/2) | 0.999 | 0.998 | 0.716 |
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 |