6UMT
High-affinity human PD-1 PD-L2 complex
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRL BEAMLINE BL12-2 |
Synchrotron site | SSRL |
Beamline | BL12-2 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2019-07-17 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.979 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 41.291, 67.798, 89.701 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 37.508 - 1.986 |
R-factor | 0.2012 |
Rwork | 0.198 |
R-free | 0.22620 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | PDB entries 3RRQ & 3BP5 |
RMSD bond length | 0.014 |
RMSD bond angle | 1.910 |
Data reduction software | HKL-3000 |
Data scaling software | HKL-3000 |
Phasing software | PHENIX |
Refinement software | PHENIX (1.9_1692) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 2.020 |
High resolution limit [Å] | 1.986 | 5.400 | 1.990 |
Rmerge | 0.146 | 0.119 | 0.761 |
Rmeas | 0.155 | 0.127 | 0.827 |
Rpim | 0.051 | 0.043 | 0.315 |
Number of reflections | 17793 | 1015 | 774 |
<I/σ(I)> | 5.9 | ||
Completeness [%] | 98.4 | 99.8 | 87.7 |
Redundancy | 8.5 | 8.7 | 5.7 |
CC(1/2) | 0.988 | 0.762 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 200 mM magnesium acetate, 10% w/v PEG8000 |