5PKI
PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 103)
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 | 71.428, 71.428, 150.467 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 29.400 - 1.190 |
| R-factor | 0.1605 |
| Rwork | 0.160 |
| R-free | 0.17850 |
| Structure solution method | FOURIER SYNTHESIS |
| Starting model (for MR) | 4d6r |
| RMSD bond length | 0.029 |
| RMSD bond angle | 2.434 |
| 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] | 29.400 | 29.400 | 1.210 |
| High resolution limit [Å] | 1.190 | 6.520 | 1.190 |
| Rmerge | 0.057 | 0.046 | 0.603 |
| Rmeas | 0.060 | 0.048 | 0.821 |
| Rpim | 0.017 | 0.015 | 0.552 |
| Total number of observations | 1112172 | 10311 | 2004 |
| Number of reflections | 112008 | ||
| <I/σ(I)> | 21.4 | 55.6 | 1.1 |
| Completeness [%] | 89.7 | 99 | 26.4 |
| Redundancy | 9.9 | 11.3 | 1.3 |
| CC(1/2) | 0.998 | 0.983 | 0.454 |
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 |
