5VCJ
Structure of alpha-galactosylphytosphingosine bound by CD1d and in complex with the Va14Vb8.2 TCR
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRL BEAMLINE BL9-2 |
Synchrotron site | SSRL |
Beamline | BL9-2 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2017-02-01 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 0.9790 |
Spacegroup name | C 2 2 21 |
Unit cell lengths | 79.261, 191.611, 151.249 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 95.810 - 3.160 |
R-factor | 0.1916 |
Rwork | 0.189 |
R-free | 0.24850 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2q7y 3quz |
RMSD bond length | 0.007 |
RMSD bond angle | 1.151 |
Data reduction software | HKL-2000 |
Data scaling software | SCALEPACK |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0158) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 95.820 | 40.000 | 3.260 |
High resolution limit [Å] | 3.150 | 6.780 | 3.150 |
Rmerge | 0.172 | 0.088 | 0.441 |
Rmeas | 0.192 | 0.098 | 0.505 |
Rpim | 0.083 | 0.042 | 0.238 |
Number of reflections | 19762 | ||
<I/σ(I)> | 3.5 | ||
Completeness [%] | 98.4 | 97.8 | 96.4 |
Redundancy | 5 | 5.1 | 4.2 |
CC(1/2) | 0.988 | 0.797 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 5 | 295 | 20 % polyethylene glycol 3350, 200 mM sodium malonate |