6DXH
Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with 4-(4-tert-butylphenyl)-4-oxobutanoate
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | ROTATING ANODE |
Source details | RIGAKU FR-E SUPERBRIGHT |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2018-05-23 |
Detector | RIGAKU SATURN A200 |
Wavelength(s) | 1.54178 |
Spacegroup name | I 2 2 2 |
Unit cell lengths | 47.690, 81.500, 99.660 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 31.560 - 2.000 |
R-factor | 0.2156 |
Rwork | 0.214 |
R-free | 0.25120 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | pdbid 2G43 |
RMSD bond length | 0.012 |
RMSD bond angle | 1.560 |
Data reduction software | xia2 |
Data scaling software | Aimless (0.7.1) |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0230) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 31.540 | 31.540 | 2.050 |
High resolution limit [Å] | 2.000 | 8.950 | 2.000 |
Rmerge | 0.054 | 0.024 | 0.451 |
Rmeas | 0.059 | 0.026 | 0.487 |
Rpim | 0.022 | 0.011 | 0.183 |
Total number of observations | 93762 | 998 | 6663 |
Number of reflections | 13422 | 180 | 957 |
<I/σ(I)> | 23 | 60.4 | 4.4 |
Completeness [%] | 99.4 | 97.5 | 98.3 |
Redundancy | 7 | 5.5 | 7 |
CC(1/2) | 1.000 | 0.999 | 0.963 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 291 | 1.5 M ammonium sulfate, 0.1 M bis-tris pH 7.0, 25% ethylene glycol (v/v), 2.25% DMSO (v/v) |