8GV2
Crystal structure of anti-FX IgG fab without 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 | 85.512, 62.289, 81.589 |
Unit cell angles | 90.00, 106.15, 90.00 |
Refinement procedure
Resolution | 49.630 - 1.274 |
R-factor | 0.1956 |
Rwork | 0.195 |
R-free | 0.21500 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5dk3 |
RMSD bond length | 0.013 |
RMSD bond angle | 1.260 |
Data reduction software | XDS (Jan 31, 2020) |
Data scaling software | Aimless (0.7.7) |
Phasing software | PHASER |
Refinement software | BUSTER (2.11.8 (8-JUN-2022)) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 49.632 | 49.632 | 1.348 |
High resolution limit [Å] | 1.274 | 3.643 | 1.274 |
Rmerge | 0.041 | 0.027 | 0.900 |
Rmeas | 0.047 | 0.031 | 1.036 |
Rpim | 0.022 | 0.015 | 0.508 |
Total number of observations | 404396 | 19777 | 18892 |
Number of reflections | 93973 | 4698 | 4697 |
<I/σ(I)> | 14.32 | 43.78 | 1.36 |
Completeness [%] | 94.2 | 99.5 | 51.3 |
Completeness (spherical) [%] | 87.6 | 99.5 | 28.4 |
Completeness (ellipsoidal) [%] | 94.2 | 99.5 | 51.3 |
Redundancy | 4.3 | 4.21 | 4.02 |
CC(1/2) | 0.999 | 0.998 | 0.545 |
Anomalous completeness (spherical) | 84.7 | 97.9 | 27.4 |
Anomalous completeness | 91.2 | 97.9 | 49.6 |
Anomalous redundancy | 2.2 | 2.2 | 2.1 |
CC(ano) | -0.165 | -0.200 | -0.020 |
|DANO|/σ(DANO) | 0.7 | 0.7 | 0.7 |
Diffraction limits | Principal axes of ellipsoid fitted to diffraction cut-off surface |
1.273 Å | 0.811, 0.811, 0.811 |
1.310 Å | 0.000, 0.000, 0.000 |
1.339 Å | 0.586, 0.586, 0.586 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 20.0 %w/v Polyethylene glycol 3350 [PEG 3350], 0.2 M Potassium formate [KFormate] |