7CJ2
Crystal structure of the Fab antibody complexed with human YKL-40
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SPRING-8 BEAMLINE BL44XU |
Synchrotron site | SPring-8 |
Beamline | BL44XU |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2020-02-02 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.9 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 89.583, 132.526, 160.007 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 45.830 - 2.700 |
R-factor | 0.2149 |
Rwork | 0.212 |
R-free | 0.26920 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1hjx 5veb |
RMSD bond length | 0.009 |
RMSD bond angle | 1.050 |
Data reduction software | XDS (v1.0.5) |
Data scaling software | XDS (v1.0.5) |
Phasing software | PHENIX (1.17.1_3660) |
Refinement software | PHENIX (1.17.1_3660) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 45.830 | 2.480 |
High resolution limit [Å] | 2.450 | 2.450 |
Rmerge | 0.092 | 0.075 |
Rmeas | 0.100 | |
Rpim | 0.038 | |
Number of reflections | 70738 | 70634 |
<I/σ(I)> | 9.4 | |
Completeness [%] | 99.8 | |
Redundancy | 6.8 | |
CC(1/2) | 0.999 | 0.999 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | MICROBATCH | 6.5 | 293.15 | 0.6M Sodium Chloride, 0.1M MES:NaOH, pH 6.5, 20% (w/v)PEG 4000, 1.0M NDSB-256 |