8F87
Crystal structure of Ebola Zaire envelope glycoprotein GP in complex with compound ARN75092
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5 | 291 | Proplex E2: 8% PEG8000, 0.1 M citrate, pH 5.0, 6.9 mg/mL EbzaA.19907.a.HE11.PD38351, plate: 12752-well E2 drop 2, Puck: PSL-1001, cryoprotectant: 16% PEG8000, 20% glycerol, 0.08 M citrate, pH 5.0, originally obtained from the complex with ARN75231, crystals were soaked in 5 mM ARN75092, 16% PEG8000, 0.1 M citrate, pH 5.0 for 24 hours before freezing |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.68 | 66.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 113.199 | α = 90 |
b = 113.199 | β = 90 |
c = 306.021 | γ = 120 |
Symmetry | |
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Space Group | H 3 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 291 | PIXEL | DECTRIS EIGER2 XE 9M | 2022-08-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 19-ID | 0.97949 | NSLS-II | 19-ID |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.6 | 93.36 | 100 | 0.101 | 0.103 | 0.022 | 0.999 | 22.2 | 21.3 | 23674 |
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) | ||||||||
1 | 2.6 | 2.67 | 100 | 1.406 | 1.44 | 0.312 | 0.928 | 21.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | PDB entry 6NAE | 2.6 | 51 | 1.34 | 23620 | 1113 | 99.78 | 0.2181 | 0.2176 | 0.2282 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.321 |
f_angle_d | 0.581 |
f_chiral_restr | 0.048 |
f_plane_restr | 0.007 |
f_bond_d | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2710 |
Nucleic Acid Atoms | |
Solvent Atoms | 11 |
Heterogen Atoms | 151 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
Aimless | data scaling |
XDS | data reduction |
PHASER | phasing |