7X4O
Crystal structure of Vps17p PX from S. cerevisiae (Space)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SPRING-8 BEAMLINE BL12B2 |
Synchrotron site | SPring-8 |
Beamline | BL12B2 |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2004-11-28 |
Detector | ADSC QUANTUM 4 |
Wavelength(s) | 1.000 |
Spacegroup name | P 21 3 |
Unit cell lengths | 100.280, 100.280, 100.280 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 44.850 - 2.020 |
R-factor | 0.2024 |
Rwork | 0.200 |
R-free | 0.25160 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | AlphaFold2 |
RMSD bond length | 0.008 |
RMSD bond angle | 0.907 |
Data reduction software | iMOSFLM (v7.2.2) |
Data scaling software | Aimless (v0.7.7) |
Phasing software | MOLREP (v11.7.3) |
Refinement software | PHENIX (1.18.2_3874) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 44.850 | 2.070 |
High resolution limit [Å] | 2.020 | 2.020 |
Rmerge | 0.088 | 0.909 |
Rmeas | 0.124 | |
Rpim | 0.088 | 0.561 |
Number of reflections | 22287 | 1603 |
<I/σ(I)> | 7.4 | 1.5 |
Completeness [%] | 97.7 | 99.6 |
Redundancy | 1.9 | 3.5 |
CC(1/2) | 0.992 | 0.548 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | COUNTER-DIFFUSION | 7.5 | 293 | 1.5M lithium sulfate, 0.1 M HEPES-Na, under a microgravity environment |