2AOC
Crystal structure analysis of HIV-1 protease mutant I84V with a substrate analog P2-NC
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1FG6 | PDB Entry 1FG6 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.4 | 293 | SODIUM CHLORIDE 0.4M, DMSO 5%, CITRATE PHOSPHATE BUFFER PH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.25 | 45.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.802 | α = 90 |
b = 85.589 | β = 90 |
c = 46.461 | 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 | ADSC QUANTUM 4 | Pt-coated toroidal Si mirror | 2002-11-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X26C | NSLS | X26C |
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 | 1.3 | 50 | 95.9 | 0.079 | 14.4 | 6.6 | 57616 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.3 | 1.35 | 72.4 | 0.33 | 3.2 | 2.9 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R | PDB Entry 1FG6 | 1.3 | 10 | 55009 | 47767 | 2761 | 96 | 0.1264 | 0.1234 | 0.1659 | 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 |
24 | 1659 | 1795.26 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_non_zero_chiral_vol | 0.089 |
s_approx_iso_adps | 0.085 |
s_zero_chiral_vol | 0.075 |
s_similar_adp_cmpnt | 0.037 |
s_from_restr_planes | 0.0307 |
s_angle_d | 0.03 |
s_anti_bump_dis_restr | 0.029 |
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 | 1510 |
Nucleic Acid Atoms | |
Solvent Atoms | 239 |
Heterogen Atoms | 83 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
HKL-2000 | data reduction |
SHELX | model building |
SHELXL-97 | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
SHELX | phasing |