5PKM
PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 107)
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 | 71.241, 71.241, 150.307 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 29.330 - 1.370 |
| R-factor | 0.1546 |
| Rwork | 0.153 |
| R-free | 0.17590 |
| Structure solution method | FOURIER SYNTHESIS |
| Starting model (for MR) | 4d6r |
| RMSD bond length | 0.027 |
| RMSD bond angle | 2.444 |
| 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] | 29.330 | 29.330 | 1.400 |
| High resolution limit [Å] | 1.370 | 7.260 | 1.370 |
| Rmerge | 0.076 | 0.056 | 0.713 |
| Rmeas | 0.079 | 0.059 | 0.776 |
| Rpim | 0.022 | 0.018 | 0.300 |
| Total number of observations | 987962 | 7301 | 25868 |
| Number of reflections | 81661 | ||
| <I/σ(I)> | 18.4 | 39.6 | 2.4 |
| Completeness [%] | 99.8 | 98.6 | 95.7 |
| Redundancy | 12.1 | 11 | 6.3 |
| CC(1/2) | 0.998 | 0.987 | 0.785 |
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 |
