8PMY
HEV gt3 P domain in complex with glycan-insensitive nAb p60.15
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3RKC |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 293 | 11% w/v PEG 8000, 0.1M Zinc acetate and 0.1M MES pH 5.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.19 | α = 90 |
b = 122.95 | β = 90 |
c = 158.67 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 X 16M | 2021-06-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, DESY BEAMLINE P11 | 0.99987 | PETRA III, DESY | P11 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim 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 | 2.406 | 48.64 | 99.61 | 0.293 | 0.993 | 7.43 | 13.12 | 21742 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.406 | 2.492 | 0.482 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2.406 | 48.65 | 21738 | 1087 | 99.8 | 0.2135 | 0.2116 | 0.2504 | RANDOM | 58.19 |
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] | |
-13.468 | 24.3157 | -10.8477 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
t_other_torsion | 16.21 |
t_omega_torsion | 3.43 |
t_angle_deg | 0.96 |
t_bond_d | 0.007 |
t_dihedral_angle_d | |
t_gen_planes | |
t_it | |
t_chiral_improper_torsion | |
t_ideal_dist_contact |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2888 |
Nucleic Acid Atoms | |
Solvent Atoms | 107 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
XDS | data reduction |
pointless | data scaling |
PHASER | phasing |