8GV1
Crystal structure of anti-FX IgG fab with FAST-Ig mutations
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SPRING-8 BEAMLINE BL45XU |
Synchrotron site | SPring-8 |
Beamline | BL45XU |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-10-23 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 1.00000 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 84.890, 62.298, 81.636 |
Unit cell angles | 90.00, 105.55, 90.00 |
Refinement procedure
Resolution | 49.560 - 1.186 |
R-factor | 0.2069 |
Rwork | 0.206 |
R-free | 0.22650 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5dk3 |
RMSD bond length | 0.008 |
RMSD bond angle | 1.040 |
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] | 49.558 | 49.558 | 1.289 |
High resolution limit [Å] | 1.186 | 3.508 | 1.186 |
Rmerge | 0.036 | 0.025 | 0.967 |
Rmeas | 0.041 | 0.028 | 1.069 |
Rpim | 0.018 | 0.013 | 0.452 |
Total number of observations | 495020 | 23784 | 28790 |
Number of reflections | 104460 | 5223 | 5226 |
<I/σ(I)> | 11.42 | 28.89 | 1.44 |
Completeness [%] | 93.5 | 99.4 | 57.2 |
Completeness (spherical) [%] | 78.8 | 99.4 | 17.8 |
Completeness (ellipsoidal) [%] | 93.5 | 99.4 | 57.2 |
Redundancy | 4.74 | 4.55 | 5.51 |
CC(1/2) | 0.999 | 0.999 | 0.610 |
Anomalous completeness (spherical) | 76.8 | 98.1 | 17.6 |
Anomalous completeness | 91.3 | 98.1 | 57.1 |
Anomalous redundancy | 2.4 | 2.4 | 2.8 |
CC(ano) | -0.117 | -0.126 | 0.011 |
|DANO|/σ(DANO) | 0.6 | 0.4 | 0.6 |
Diffraction limits | Principal axes of ellipsoid fitted to diffraction cut-off surface |
1.186 Å | 0.854, 0.854, 0.854 |
1.300 Å | 0.000, 0.000, 0.000 |
1.293 Å | -0.521, -0.521, -0.521 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.2 M Sodium acetate trihydrate [NaAcet], 20.0 %w/v Polyethylene glycol 3350 [PEG 3350] |