2JE4
Atomic-resolution crystal structure of chemically-synthesized HIV-1 protease in complex with JG-365
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7HVP | PDB ENTRY 7HVP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | well solution 0.1 M citrate, 0.2 M sodium phosphate, 30% saturated ammonium sulfate, and 10% DMSO, pH 6.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.03 | 39.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.501 | α = 90 |
b = 58.853 | β = 90 |
c = 60.886 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 150 | M | SINGLE WAVELENGTH | |||||||||
2 | 1 | x-ray | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 14-BM-C | APS | 14-BM-C | |
2 | SYNCHROTRON | APS BEAMLINE 19-BM | APS | 19-BM |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.07 | 50 | 93.9 | 0.062 | 28.2 | 6.2 | 72978 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.07 | 1.11 | 82.8 | 0.332 | 2.9 | 2.9 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | PDB ENTRY 7HVP | 1.07 | 10 | 75585 | 3830 | 93.9 | 0.144 | 0.143 | 0.184 | RANDOM |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
44 | 1379.92 | 1791.98 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_zero_chiral_vol | 0.106 |
s_approx_iso_adps | 0.098 |
s_non_zero_chiral_vol | 0.087 |
s_similar_adp_cmpnt | 0.061 |
s_anti_bump_dis_restr | 0.043 |
s_angle_d | 0.039 |
s_from_restr_planes | 0.035 |
s_bond_d | 0.016 |
s_rigid_bond_adp_cmpnt | 0.007 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1567 |
Nucleic Acid Atoms | |
Solvent Atoms | 394 |
Heterogen Atoms | 59 |
Software
Software | |
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Software Name | Purpose |
SHELXL-97 | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |