5PKB
PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 96)
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 | 71.131, 71.131, 149.862 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 29.280 - 1.400 |
R-factor | 0.1623 |
Rwork | 0.161 |
R-free | 0.18640 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 4d6r |
RMSD bond length | 0.026 |
RMSD bond angle | 2.407 |
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] | 29.280 | 29.280 | 1.420 |
High resolution limit [Å] | 1.400 | 7.400 | 1.400 |
Rmerge | 0.063 | 0.043 | 0.699 |
Rmeas | 0.066 | 0.045 | 0.748 |
Rpim | 0.018 | 0.014 | 0.259 |
Total number of observations | 955119 | 6879 | 30660 |
Number of reflections | 76673 | ||
<I/σ(I)> | 22.7 | 53 | 2.8 |
Completeness [%] | 99.9 | 98.5 | 98 |
Redundancy | 12.5 | 10.8 | 7.8 |
CC(1/2) | 0.999 | 0.997 | 0.834 |
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 |