5PNE
PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 208)
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 | 71.651, 71.651, 150.636 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 29.490 - 1.290 |
| R-factor | 0.161 |
| Rwork | 0.160 |
| R-free | 0.17970 |
| Structure solution method | FOURIER SYNTHESIS |
| Starting model (for MR) | 4d6r |
| RMSD bond length | 0.028 |
| RMSD bond angle | 2.424 |
| 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] | 29.490 | 29.490 | 1.310 |
| High resolution limit [Å] | 1.290 | 7.060 | 1.290 |
| Rmerge | 0.108 | 0.084 | 0.695 |
| Rmeas | 0.112 | 0.088 | 0.768 |
| Rpim | 0.032 | 0.026 | 0.320 |
| Total number of observations | 1170882 | 8805 | 24692 |
| Number of reflections | 99146 | ||
| <I/σ(I)> | 14 | 31.8 | 2.2 |
| Completeness [%] | 99.8 | 98.7 | 96.8 |
| Redundancy | 11.8 | 12 | 5.3 |
| CC(1/2) | 0.996 | 0.985 | 0.767 |
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 |
