6YVK
Human OMPD-domain of UMPS in complex with the substrate OMP at 1.25 Angstroms resolution, 0.71 MGy exposure
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) |
Synchrotron site | PETRA III, EMBL c/o DESY |
Beamline | P14 (MX2) |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-07-08 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.82660 |
Spacegroup name | C 2 2 21 |
Unit cell lengths | 77.290, 116.820, 61.950 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 19.670 - 1.250 |
R-factor | 0.1322 |
Rwork | 0.131 |
R-free | 0.15500 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2qcd |
RMSD bond length | 0.009 |
RMSD bond angle | 1.503 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | MOLREP |
Refinement software | REFMAC (5.8.0258) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 19.670 | 20.000 | 1.300 |
High resolution limit [Å] | 1.250 | 10.000 | 1.250 |
Rmerge | 0.079 | 0.017 | 1.237 |
Rmeas | 0.085 | 0.018 | 1.338 |
Total number of observations | 528065 | ||
Number of reflections | 77475 | 155 | 8513 |
<I/σ(I)> | 15.94 | 79.87 | 1.9 |
Completeness [%] | 99.8 | 98.7 | 99.9 |
Redundancy | 6.816 | 5.129 | 6.835 |
CC(1/2) | 0.999 | 1.000 | 0.717 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | Crystallization: 100 mM Tris/HCl pH 8.0, 1.9 - 2.1 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol Soaking: 100 mM Tris/HCl pH 8.0, 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 50 mM OMP Cryo-protection: 100 mM Tris/HCl pH 8.0, 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 50 mM OMP |