3RRQ
Crystal structure of the extracellular domain of human PD-1
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | NSLS BEAMLINE X29A |
Synchrotron site | NSLS |
Beamline | X29A |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2008-01-01 |
Detector | ADSC QUANTUM 315 |
Wavelength(s) | 0.979 |
Spacegroup name | P 65 2 2 |
Unit cell lengths | 46.020, 46.020, 187.395 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 36.690 - 2.100 |
R-factor | 0.2159 |
Rwork | 0.214 |
R-free | 0.24880 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1npu |
RMSD bond length | 0.013 |
RMSD bond angle | 1.501 |
Data reduction software | HKL-2000 |
Data scaling software | SCALEPACK |
Phasing software | MOLREP |
Refinement software | REFMAC |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 2.180 |
High resolution limit [Å] | 2.100 | 4.520 | 2.100 |
Rmerge | 0.066 | 0.026 | 0.572 |
Number of reflections | 7612 | ||
<I/σ(I)> | 9.1 | ||
Completeness [%] | 99.9 | 99.3 | 100 |
Redundancy | 17.4 | 14.9 | 18.3 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 298 | 3.5M Sodium formate, 0.1M Bis-Tris, pH 7.5, Vapor diffusion, Sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP |