7PDY
A viral peptide from Marek's disease virus bound to chicken MHC-II molecule
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | DIAMOND BEAMLINE I04-1 |
| Synchrotron site | Diamond |
| Beamline | I04-1 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2018-03-10 |
| Detector | DECTRIS PILATUS 6M-F |
| Wavelength(s) | 0.920 |
| Spacegroup name | P 32 2 1 |
| Unit cell lengths | 238.538, 238.538, 76.521 |
| Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
| Resolution | 206.580 - 2.540 |
| R-factor | 0.2175 |
| Rwork | 0.216 |
| R-free | 0.25180 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 6kvm |
| RMSD bond length | 0.007 |
| RMSD bond angle | 1.470 |
| Data reduction software | xia2 |
| Data scaling software | Aimless (0.5.32) |
| Phasing software | PHASER |
| Refinement software | REFMAC (5.8.0267) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 206.580 | 206.580 | 2.680 |
| High resolution limit [Å] | 2.540 | 8.040 | 2.540 |
| Rmerge | 0.138 | 0.043 | 4.430 |
| Rmeas | 0.142 | 0.044 | 4.540 |
| Rpim | 0.031 | 0.010 | 0.988 |
| Total number of observations | 1686668 | 53267 | 231659 |
| Number of reflections | 81291 | 2730 | 11155 |
| <I/σ(I)> | 16.6 | 62.7 | 0.8 |
| Completeness [%] | 99.1 | 99.8 | 93.8 |
| Redundancy | 20.7 | 19.5 | 20.8 |
| CC(1/2) | 0.999 | 0.998 | 0.405 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 293 | PEG 4000, sodium acetate |
