2AOH
Crystal structure analysis of HIV-1 Protease mutant V82A with a substrate analog P6-PR
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1DAZ | PDB ENTRY 1DAZ |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 293 | AMMONIUM SULFATE 30%, DMSO 7%,SODIUM ACETATE BUFFER, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.61 | 52.9 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 58.882 | α = 90 |
b = 86.283 | β = 90 |
c = 46.404 | γ = 90 |
Symmetry | |
---|---|
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 | 90 | CCD | ADSC QUANTUM 315 | 2002-11-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X26C | 0.97900 | NSLS | X26C |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.42 | 50 | 90.3 | 0.098 | 17.1 | 5.1 | 45584 |
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 | 1.42 | 1.47 | 100 | 0.708 | 2.63 | 4.9 |
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 1DAZ | 1.42 | 10 | 40847 | 34360 | 2043 | 90.3 | 0.1818 | 0.1788 | 0.2328 | 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 |
18 | 1788.1 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
s_approx_iso_adps | 0.087 |
s_non_zero_chiral_vol | 0.077 |
s_zero_chiral_vol | 0.067 |
s_similar_adp_cmpnt | 0.037 |
s_from_restr_planes | 0.0342 |
s_angle_d | 0.031 |
s_anti_bump_dis_restr | 0.015 |
s_bond_d | 0.011 |
s_rigid_bond_adp_cmpnt | 0.003 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1586 |
Nucleic Acid Atoms | |
Solvent Atoms | 240 |
Heterogen Atoms | 3 |
Software
Software | |
---|---|
Software Name | Purpose |
HKL-2000 | data collection |
HKL-2000 | data reduction |
SHELX | model building |
SHELXL-97 | refinement |
MAR345 | data collection |
HKL-2000 | data scaling |
AMoRE | phasing |