6YWT
Human OMPD-domain of UMPS (K314AcK) in complex with 6-hydroxy-UMP at 1.05 Angstroms resolution
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 | 2019-05-30 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.82660 |
Spacegroup name | C 2 2 21 |
Unit cell lengths | 77.390, 116.840, 62.040 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 19.700 - 1.050 |
R-factor | 0.1215 |
Rwork | 0.121 |
R-free | 0.13910 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2qcd |
RMSD bond length | 0.011 |
RMSD bond angle | 1.783 |
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] | 19.700 | 20.000 | 1.100 |
High resolution limit [Å] | 1.050 | 10.000 | 1.050 |
Rmerge | 0.062 | 0.027 | 1.095 |
Rmeas | 0.067 | 0.031 | 1.200 |
Total number of observations | 866329 | ||
Number of reflections | 130413 | 148 | 16784 |
<I/σ(I)> | 14.9 | 56.53 | 1.91 |
Completeness [%] | 99.9 | 93.7 | 99.7 |
Redundancy | 6.643 | 4.622 | 5.978 |
CC(1/2) | 1.000 | 0.997 | 0.714 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | Crystallization: 100 mM Tris/HCl pH 7.8, 1.6 - 1.8 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 5mg/mL OMPD, 12 mM BMP Cryo-protection: 100 mM Tris/HCl pH 7.8, 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 12 mM BMP, 2 M L-proline |