7TO5
HIV-1 wild type protease with GRL-05816A, with C-4 substituted cyclohexane-fused bis-tetrahydrofuran (Chf-THF) derivatives as P2-ligand [diastereomer 1]
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3NU3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 298 | 0.5 M NaCl, 0.1M Sodium Acetate, pH 6.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.72 | 54.84 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.943 | α = 90 |
b = 86.138 | β = 90 |
c = 46.097 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | 2021-06-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1 | APS | 22-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) | 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 | 1.13 | 50 | 91.6 | 0.06 | 0.063 | 0.018 | 24.5 | 8.8 | 80849 |
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 | 1.13 | 1.17 | 52.1 | 0.41 | 0.482 | 0.248 | 0.868 | 3.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 3NU3 | 1.13 | 36.34 | 76823 | 3976 | 91.48 | 0.1236 | 0.1226 | 0.1422 | RANDOM | 12.164 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
0.44 | -0.26 | -0.18 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.199 |
r_dihedral_angle_4_deg | 14.643 |
r_dihedral_angle_3_deg | 10.995 |
r_dihedral_angle_1_deg | 6.723 |
r_rigid_bond_restr | 4.866 |
r_angle_refined_deg | 2.701 |
r_angle_other_deg | 1.524 |
r_chiral_restr | 0.907 |
r_bond_refined_d | 0.023 |
r_gen_planes_refined | 0.014 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1512 |
Nucleic Acid Atoms | |
Solvent Atoms | 279 |
Heterogen Atoms | 111 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |