7TAZ
Crystal structure of HIV-1 reverse transcriptase (RT) in complex with VM-1500A, a non-nucleoside RT inhibitor
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.4 | 277 | PEG 8,000, ammonium sulfate, Bis tris propane, ethylene glycol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.55 | 51.81 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 163.05 | α = 90 |
b = 73.87 | β = 99.96 |
c = 108.64 | 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 | 2020-12-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 1.03321 | 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 | 2.4 | 48.62 | 99.9 | 0.049 | 0.053 | 0.02 | 0.999 | 19.8 | 6.8 | 49968 |
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 | 2.4 | 2.48 | 100 | 0.769 | 0.831 | 0.313 | 0.876 | 7 |
Refinement
Statistics | |||||||||||||||||||
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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 | 4G1Q | 2.4 | 48.62 | 47489 | 2478 | 99.92 | 0.2239 | 0.2233 | 0.2362 | RANDOM | 88.277 |
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] | |
-2.54 | -1.81 | -0.73 | 3.68 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.528 |
r_dihedral_angle_3_deg | 17.056 |
r_dihedral_angle_4_deg | 14.7 |
r_dihedral_angle_1_deg | 7.662 |
r_angle_other_deg | 2.245 |
r_angle_refined_deg | 1.532 |
r_chiral_restr | 0.067 |
r_bond_other_d | 0.034 |
r_gen_planes_other | 0.009 |
r_bond_refined_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7955 |
Nucleic Acid Atoms | |
Solvent Atoms | 276 |
Heterogen Atoms | 33 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |