7XL0
Crystal structure of Vobarilizumab at 1.70 Angstrom
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.2 M lithium sulfate 20% PEG 3,350 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.58 | 52.31 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 124.591 | α = 90 |
b = 56.42 | β = 101.92 |
c = 42.24 | γ = 90 |
Symmetry | |
---|---|
Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER R 4M | 2019-03-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-1A | 1.000 | Photon Factory | BL-1A |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.7 | 52 | 98.9 | 0.092 | 0.04 | 0.995 | 11.5 | 6 | 31315 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.7 | 1.79 | 0.336 | 0.16 | 0.89 | 4.4 |
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 | 5HVG | 1.7 | 51.25 | 30038 | 1275 | 98.89 | 0.1539 | 0.1521 | 0.1963 | RANDOM | 25.895 |
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] | |
0.02 | 0.29 | 0.01 | -0.14 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.849 |
r_dihedral_angle_4_deg | 13.479 |
r_dihedral_angle_3_deg | 12.259 |
r_dihedral_angle_1_deg | 7.363 |
r_angle_refined_deg | 1.353 |
r_angle_other_deg | 1.295 |
r_rigid_bond_restr | 1.113 |
r_chiral_restr | 0.058 |
r_bond_refined_d | 0.006 |
r_gen_planes_refined | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1814 |
Nucleic Acid Atoms | |
Solvent Atoms | 188 |
Heterogen Atoms | 16 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |