6XS5
Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-D1
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 |
Synchrotron site | Australian Synchrotron |
Beamline | MX2 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-09-23 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.953729 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 114.390, 43.770, 43.140 |
Unit cell angles | 90.00, 100.53, 90.00 |
Refinement procedure
Resolution | 42.410 - 2.010 |
R-factor | 0.192184947795 |
Rwork | 0.190 |
R-free | 0.22531 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1w24 |
RMSD bond length | 0.007 |
RMSD bond angle | 1.210 |
Data reduction software | XDS |
Data scaling software | Aimless (0.7.2) |
Phasing software | PHASER (2.5.6) |
Refinement software | PHENIX (1.10.1) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 42.410 | 2.060 |
High resolution limit [Å] | 2.010 | 2.010 |
Rmerge | 0.077 | 0.585 |
Rmeas | 0.083 | 0.632 |
Rpim | 0.032 | 0.235 |
Number of reflections | 14169 | 1030 |
<I/σ(I)> | 12.2 | 2.5 |
Completeness [%] | 99.9 | 98.8 |
Redundancy | 6.9 | 7 |
CC(1/2) | 0.999 | 0.917 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 3.5 M Sodium Formate |