6YVO
Human OMPD-domain of UMPS in complex with the substrate OMP at 1.25 Angstroms resolution, 3.55 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 | 77.390, 116.900, 62.000 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 19.690 - 1.250 |
R-factor | 0.137 |
Rwork | 0.136 |
R-free | 0.16490 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2qcd |
RMSD bond length | 0.009 |
RMSD bond angle | 1.483 |
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] | 19.690 | 20.000 | 1.300 |
High resolution limit [Å] | 1.250 | 10.000 | 1.250 |
Rmerge | 0.086 | 0.016 | 1.941 |
Rmeas | 0.094 | 0.018 | 2.100 |
Total number of observations | 530011 | ||
Number of reflections | 77696 | 155 | 8538 |
<I/σ(I)> | 14.33 | 81.8 | 1.19 |
Completeness [%] | 99.8 | 98.1 | 99.8 |
Redundancy | 6.822 | 5.11 | 6.843 |
CC(1/2) | 0.999 | 1.000 | 0.511 |
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 |