4KB9
Crystal structure of wild-type HIV-1 protease with novel tricyclic P2-ligands GRL-0739A
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3NU3 | PDB ENTRY 3NU3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 298 | 1.15 M NaCl + 0.1 M Na acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.32 | 54.52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.477 | α = 90 |
b = 86.3 | β = 90 |
c = 46.045 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | CCD | MARMOSAIC 225 mm CCD | 2012-10-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-BM | APS | 22-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 | 1.29 | 50 | 92.6 | 0.061 | 21.9 | 6.5 | 56283 | 56283 | 13.2 |
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 | 1.29 | 1.34 | 54.7 | 0.436 | 2 | 2.5 | 3275 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | 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 | PDB ENTRY 3NU3 | 1.29 | 10 | 55418 | 55418 | 2770 | 93.5 | 0.1416 | 0.1394 | 0.1394 | 0.1799 | RANDOM |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
25 | 1645 | 1741.25 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_approx_iso_adps | 0.082 |
s_non_zero_chiral_vol | 0.071 |
s_zero_chiral_vol | 0.07 |
s_similar_adp_cmpnt | 0.052 |
s_angle_d | 0.032 |
s_from_restr_planes | 0.0295 |
s_anti_bump_dis_restr | 0.028 |
s_bond_d | 0.013 |
s_rigid_bond_adp_cmpnt | 0.004 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1512 |
Nucleic Acid Atoms | |
Solvent Atoms | 220 |
Heterogen Atoms | 70 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
PHASES | phasing |
SHELXL-97 | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |