8W85
HLA-DQ2.5-gamma2 gliadin peptide in complex with DQN0385AE01
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PHOTON FACTORY BEAMLINE BL-1A |
Synchrotron site | Photon Factory |
Beamline | BL-1A |
Temperature [K] | 95 |
Detector technology | PIXEL |
Collection date | 2018-12-05 |
Detector | DECTRIS EIGER X 4M |
Wavelength(s) | 1.10000 |
Spacegroup name | C 2 2 2 |
Unit cell lengths | 150.525, 243.913, 136.081 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 50.470 - 2.769 |
R-factor | 0.2554 |
Rwork | 0.253 |
R-free | 0.29990 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 7VG1 |
RMSD bond length | 0.008 |
RMSD bond angle | 1.050 |
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] | 136.081 | 136.081 | 3.105 |
High resolution limit [Å] | 2.769 | 8.886 | 2.769 |
Rmerge | 0.120 | 0.030 | 1.883 |
Rmeas | 0.124 | 0.032 | 1.956 |
Rpim | 0.034 | 0.009 | 0.524 |
Total number of observations | 571351 | 27091 | 28797 |
Number of reflections | 41787 | 2089 | 2089 |
<I/σ(I)> | 16.25 | 52.89 | 1.57 |
Completeness [%] | 94.0 | 99.6 | 64.8 |
Completeness (spherical) [%] | 65.3 | 99.6 | 11.3 |
Completeness (ellipsoidal) [%] | 94.0 | 99.6 | 64.8 |
Redundancy | 13.67 | 12.97 | 13.79 |
CC(1/2) | 0.999 | 0.999 | 0.684 |
Anomalous completeness (spherical) | 64.6 | 99.8 | 10.9 |
Anomalous completeness | 94.0 | 99.8 | 63.6 |
Anomalous redundancy | 7.1 | 7.3 | 7.2 |
CC(ano) | -0.036 | -0.030 | -0.027 |
|DANO|/σ(DANO) | 0.8 | 0.7 | 0.7 |
Diffraction limits | Principal axes of ellipsoid fitted to diffraction cut-off surface |
3.510 Å | 1.000, 1.000, 1.000 |
3.193 Å | 0.000, 0.000, 0.000 |
2.751 Å | 0.000, 0.000, 0.000 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 294 | 0.1 M Ammonium sulfate, 10.0 %w/v Polyethylene glycol 3,350, and 30 %v/v Ethylene glycol as cryoprotectant |