2QNN
HIV-1 protease in complex with a multiple decorated pyrrolidine-based inhibitor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2PQZ | pdb entry 2PQZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 2.25M NaCl, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.65 | 53.56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.384 | α = 90 |
b = 86.179 | β = 90 |
c = 46.29 | 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 | 113 | CCD | MAR CCD 165 mm | Double crystal monochromator wit 2 sets of mirrors | 2007-03-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.2 | 0.97803 | BESSY | 14.2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.48 | 25 | 99.5 | 0.048 | 4.8 | 23.5 | 3.5 | 38945 | 38945 | 13.3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.48 | 1.51 | 96.4 | 0.287 | 28.7 | 3.71 | 2.7 | 1863 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | 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 | AB INITIO | FREE R | pdb entry 2PQZ | 1.48 | 10 | 2 | 4 | 36820 | 36820 | 1924 | 94.7 | 0.1837 | 0.1699 | 0.1695 | 0.1925 | 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 |
6 | 1577 | 1698.5 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_zero_chiral_vol | 0.063 |
s_non_zero_chiral_vol | 0.059 |
s_similar_adp_cmpnt | 0.051 |
s_anti_bump_dis_restr | 0.029 |
s_from_restr_planes | 0.0284 |
s_angle_d | 0.027 |
s_bond_d | 0.009 |
s_similar_dist | |
s_rigid_bond_adp_cmpnt | |
s_approx_iso_adps |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1498 |
Nucleic Acid Atoms | |
Solvent Atoms | 134 |
Heterogen Atoms | 67 |
Software
Software | |
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Software Name | Purpose |
SHELX | model building |
SHELXL-97 | refinement |
MAR345dtb | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |