8W86
HLA-DQ2.5-B/C hordein peptide in complex with DQN0385AE02
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SPRING-8 BEAMLINE BL45XU |
Synchrotron site | SPring-8 |
Beamline | BL45XU |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2019-07-17 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 1.00000 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 73.701, 127.187, 130.365 |
Unit cell angles | 90.00, 104.45, 90.00 |
Refinement procedure
Resolution | 126.220 - 2.236 |
R-factor | 0.243 |
Rwork | 0.241 |
R-free | 0.28040 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 7VG1 |
RMSD bond length | 0.008 |
RMSD bond angle | 1.030 |
Data reduction software | XDS (Jan 31, 2020) |
Data scaling software | Aimless (0.7.7) |
Phasing software | PHASER |
Refinement software | BUSTER (2.11.8) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 126.220 | 126.220 | 2.457 |
High resolution limit [Å] | 2.236 | 6.921 | 2.236 |
Rmerge | 0.102 | 0.034 | 1.229 |
Rmeas | 0.113 | 0.037 | 1.344 |
Rpim | 0.048 | 0.016 | 0.538 |
Total number of observations | 412512 | 20792 | 23238 |
Number of reflections | 77604 | 3879 | 3880 |
<I/σ(I)> | 10.72 | 29.04 | 1.56 |
Completeness [%] | 93.6 | 99.7 | 61.4 |
Completeness (spherical) [%] | 69.1 | 99.7 | 14.0 |
Completeness (ellipsoidal) [%] | 93.6 | 99.7 | 61.4 |
Redundancy | 5.32 | 5.36 | 5.99 |
CC(1/2) | 0.998 | 0.998 | 0.511 |
Anomalous completeness (spherical) | 68.0 | 99.7 | 14.0 |
Anomalous completeness | 92.1 | 99.7 | 60.2 |
Anomalous redundancy | 2.7 | 2.8 | 3.0 |
CC(ano) | -0.073 | -0.160 | 0.020 |
|DANO|/σ(DANO) | 0.8 | 0.6 | 0.8 |
Diffraction limits | Principal axes of ellipsoid fitted to diffraction cut-off surface |
2.849 Å | 0.962, 0.962, 0.962 |
2.235 Å | 0.000, 0.000, 0.000 |
2.394 Å | -0.274, -0.274, -0.274 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 294 | 0.1 M MES monohydrate (pH5.5), 12.0 %w/v Polyethylene glycol 8,000, 0.1 M Calcium acetate hydrate, and 30 %v/v Ethylene glycol as cryoprotectant |