5PNQ
PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 220)
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 | 71.694, 71.694, 150.632 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 29.500 - 1.470 |
R-factor | 0.1676 |
Rwork | 0.166 |
R-free | 0.19280 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 4d6r |
RMSD bond length | 0.024 |
RMSD bond angle | 2.211 |
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] | 29.500 | 29.500 | 1.500 |
High resolution limit [Å] | 1.470 | 8.070 | 1.470 |
Rmerge | 0.064 | 0.035 | 0.878 |
Rmeas | 0.067 | 0.037 | 0.921 |
Rpim | 0.018 | 0.011 | 0.273 |
Total number of observations | 856533 | 5784 | 33851 |
Number of reflections | 66818 | ||
<I/σ(I)> | 25.3 | 77 | 2.9 |
Completeness [%] | 99.5 | 98.1 | 95 |
Redundancy | 12.8 | 11.5 | 11 |
CC(1/2) | 0.999 | 0.997 | 0.820 |
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 |