8FFX
Crystal structure of HIV-1 reverse transcriptase in complex with non-nucleoside inhibitor 19980
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 277 | 10%(v/v) PEG 8000, 4%(v/v) PEG 400, 100 mM imidazole pH 6.6, 10 mM spermine, 15 mM MgSO4, 100 mM ammonium sulfate, and 5 mM tris(2-carboxyethyl)phosphine |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.77 | 55.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 161.952 | α = 90 |
b = 73.377 | β = 100.05 |
c = 107.966 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 6M | 2020-03-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 1.033 | APS | 23-ID-D |
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 | 2.42 | 48.29 | 98.98 | 0.08761 | 0.1239 | 0.08761 | 0.425 | 9.75 | 2 | 47666 | 54.48 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.42 | 2.507 | 95.54 | 0.288 | 1.62 | 2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2.42 | 48.29 | 1.34 | 47356 | 1988 | 98.99 | 0.2159 | 0.2137 | 0.2656 | 82.23 |
Temperature Factor Modeling | ||||||
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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 | 18.0512 |
f_angle_d | 0.6937 |
f_chiral_restr | 0.0468 |
f_plane_restr | 0.0051 |
f_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7951 |
Nucleic Acid Atoms | |
Solvent Atoms | 123 |
Heterogen Atoms | 50 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
autoXDS | data reduction |
pointless | data scaling |
PHASER | phasing |