8AS0
PD-1 extracellular domain in complex with Fab fragment from D12 antibody
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ESRF BEAMLINE MASSIF-1 |
Synchrotron site | ESRF |
Beamline | MASSIF-1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-07-01 |
Detector | DECTRIS PILATUS3 2M |
Wavelength(s) | 0.965 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 81.195, 187.092, 190.845 |
Unit cell angles | 90.00, 90.24, 90.00 |
Refinement procedure
Resolution | 95.420 - 3.500 |
R-factor | 0.2456 |
Rwork | 0.243 |
R-free | 0.29260 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5wt9 Alphafold2 |
RMSD bond length | 0.004 |
RMSD bond angle | 0.700 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | PHENIX ((1.20_4459: ???)) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 190.840 | 3.580 |
High resolution limit [Å] | 3.500 | 3.500 |
Rmerge | 0.141 | 0.642 |
Rpim | 0.100 | 0.431 |
Number of reflections | 68755 | 4708 |
<I/σ(I)> | 3.9 | |
Completeness [%] | 96.1 | 97.6 |
Redundancy | 1.7 | 1.8 |
CC(1/2) | 0.940 | 0.431 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.5 | 293 | 22% PEG 3350, 250 mM sodium malonate, pH 4.5 |