8GV0
Crystal structure of anti-FIXa IgG fab without FAST-Ig mutations
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 5DK3 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 20.0 %w/v Polyethylene glycol 3350 [PEG 3350], 0.1 M CBTP buffer [CBTP] pH 6.4 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.38 | 48.4 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 40.937 | α = 90 |
b = 162.082 | β = 98.05 |
c = 139.014 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 95 | PIXEL | DECTRIS EIGER X 4M | 2021-12-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-1A | 1.04500 | Photon Factory | BL-1A |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||
1 | 3.192 | 137.644 | 86.4 | 0.521 | 0.5634 | 0.2122 | 0.929 | 4.1 | 7.02 | 18205 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
3.192 | 3.705 | 37.7 | 1.3761 | 1.4874 | 0.5574 | 0.552 | 1.64 | 6.77 | 911 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 5DK3 | 3.192 | 42.5 | 18195 | 855 | 61 | 0.2015 | 0.196 | 0.3098 | RANDOM | 52.42 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
2.6136 | -5.0715 | -5.0797 | 2.4661 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
t_other_torsion | 23.15 |
t_omega_torsion | 2.84 |
t_angle_deg | 1.16 |
t_bond_d | 0.009 |
t_dihedral_angle_d | |
t_gen_planes | |
t_it | |
t_chiral_improper_torsion | |
t_ideal_dist_contact |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 12276 |
Nucleic Acid Atoms | |
Solvent Atoms | 40 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
autoPROC | data processing |
XDS | data reduction |
Aimless | data scaling |
STARANISO | data scaling |
PHENIX | refinement |
PHASER | phasing |
BUSTER | refinement |