5NKZ
Crystal structure of H. polymorpha ubiquitin conjugating enzyme Pex4p in complex with soluble domain of Pex22p
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PETRA III, DESY BEAMLINE P11 |
Synchrotron site | PETRA III, DESY |
Beamline | P11 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2016-07-17 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 0.98 |
Spacegroup name | P 1 |
Unit cell lengths | 44.683, 61.582, 78.441 |
Unit cell angles | 89.18, 78.02, 84.09 |
Refinement procedure
Resolution | 48.040 - 2.850 |
R-factor | 0.2385 |
Rwork | 0.236 |
R-free | 0.28370 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | Pex4:Pex22 complex coordinates from S. cerevisae (PDB: 2Y9M(Williams et al. 2012); 33/57 % and 14/35 % identity/similarity respectively) as starting model |
RMSD bond length | 0.016 |
RMSD bond angle | 1.925 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | MOLREP |
Refinement software | REFMAC (5.8.0158) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 48.040 | 2.950 |
High resolution limit [Å] | 2.850 | 2.850 |
Rmerge | 0.123 | 0.800 |
Number of reflections | 20450 | 1822 |
<I/σ(I)> | 6.03 | 1.14 |
Completeness [%] | 95.0 | 94.5 |
Redundancy | 3.93 | 5.49 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 0.1 M BIS-TRIS Propane pH 7.8, 0.2 M sodium sulphate, 22 % w/v PEG-3350 |