5PKQ
PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 111)
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 | 71.622, 71.622, 150.473 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 29.470 - 1.280 |
| R-factor | 0.1584 |
| Rwork | 0.157 |
| R-free | 0.17960 |
| Structure solution method | FOURIER SYNTHESIS |
| Starting model (for MR) | 4d6r |
| RMSD bond length | 0.028 |
| RMSD bond angle | 2.414 |
| 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] | 29.470 | 29.470 | 1.300 |
| High resolution limit [Å] | 1.280 | 7.010 | 1.280 |
| Rmerge | 0.068 | 0.051 | 0.659 |
| Rmeas | 0.071 | 0.054 | 0.730 |
| Rpim | 0.020 | 0.016 | 0.303 |
| Total number of observations | 1083648 | 8254 | 14166 |
| Number of reflections | 93874 | ||
| <I/σ(I)> | 20 | 44.8 | 2.4 |
| Completeness [%] | 92.4 | 98.8 | 53.7 |
| Redundancy | 11.5 | 11 | 5.4 |
| CC(1/2) | 0.999 | 0.994 | 0.748 |
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 |
