5PMD
PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 171)
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 | 71.782, 71.782, 151.241 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 29.550 - 1.630 |
| R-factor | 0.1544 |
| Rwork | 0.153 |
| R-free | 0.18390 |
| Structure solution method | FOURIER SYNTHESIS |
| Starting model (for MR) | 4d6r |
| RMSD bond length | 0.023 |
| RMSD bond angle | 2.081 |
| 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] | 29.550 | 29.550 | 1.650 |
| High resolution limit [Å] | 1.630 | 8.900 | 1.630 |
| Rmerge | 0.069 | 0.030 | 0.900 |
| Rmeas | 0.071 | 0.031 | 0.947 |
| Rpim | 0.019 | 0.009 | 0.285 |
| Total number of observations | 653985 | 4314 | 23624 |
| Number of reflections | 49894 | ||
| <I/σ(I)> | 26.1 | 84.7 | 2.7 |
| Completeness [%] | 98.8 | 97.4 | 93.2 |
| Redundancy | 13.1 | 11.4 | 10.3 |
| CC(1/2) | 0.999 | 0.997 | 0.760 |
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 |
