8GUZ
Crystal structure of anti-FIXa IgG fab with FAST-Ig mutations
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PHOTON FACTORY BEAMLINE BL-1A |
Synchrotron site | Photon Factory |
Beamline | BL-1A |
Temperature [K] | 95 |
Detector technology | PIXEL |
Collection date | 2021-12-13 |
Detector | DECTRIS EIGER X 4M |
Wavelength(s) | 1.04500 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 41.270, 232.840, 41.432 |
Unit cell angles | 90.00, 93.96, 90.00 |
Refinement procedure
Resolution | 20.670 - 1.790 |
R-factor | 0.2048 |
Rwork | 0.201 |
R-free | 0.27270 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5dk3 |
RMSD bond length | 0.009 |
RMSD bond angle | 1.080 |
Data reduction software | XDS (Jan 31, 2020) |
Data scaling software | Aimless (0.7.7) |
Phasing software | PHASER |
Refinement software | PHENIX (1.20.1) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 116.420 | 116.420 | 1.935 |
High resolution limit [Å] | 1.790 | 5.050 | 1.790 |
Rmerge | 0.148 | 0.057 | 1.155 |
Rmeas | 0.163 | 0.063 | 1.245 |
Rpim | 0.069 | 0.026 | 0.465 |
Total number of observations | 300384 | 18071 | 15718 |
Number of reflections | 53046 | 3284 | 2189 |
<I/σ(I)> | 7.79 | 22.46 | 1.54 |
Completeness [%] | 91.1 | 99.9 | 60 |
Completeness (spherical) [%] | 72.7 | 99.9 | 14.5 |
Completeness (ellipsoidal) [%] | 91.1 | 99.9 | 60.0 |
Redundancy | 5.66 | 5.5 | 7.18 |
CC(1/2) | 0.994 | 0.997 | 0.653 |
Anomalous completeness (spherical) | 72.2 | 99.3 | 14.6 |
Anomalous completeness | 90.5 | 99.3 | 60.0 |
Anomalous redundancy | 2.9 | 2.8 | 3.6 |
CC(ano) | -0.093 | -0.169 | -0.017 |
|DANO|/σ(DANO) | 0.8 | 0.7 | 0.7 |
Diffraction limits | Principal axes of ellipsoid fitted to diffraction cut-off surface |
2.107 Å | 0.716, 0.716, 0.716 |
1.738 Å | 0.000, 0.000, 0.000 |
1.957 Å | -0.699, -0.699, -0.699 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.2 M Calcium chloride dihydrate [CaCl2] , 20.0 %w/v Polyethylene glycol 3350 [PEG 3350] |