1BDR
HIV-1 (2: 31, 33-37) PROTEASE COMPLEXED WITH INHIBITOR SB203386
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1SBG | PDB ENTRY 1SBG |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.2 | 294 | HANGING DROP VAPOUR DIFFUSION, BY MIXING EQUAL VOLUMES OF RESERVOIR AND SAMPLE, 21 DEG. C RESERVOIR: 28% 3.5 MG/ML PROTEIN/INHIBITOR COMPLEX AT 1:5 MOLAR RATIO., pH 5.2, vapor diffusion - hanging drop, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 45 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.68 | α = 90 |
b = 62.68 | β = 90 |
c = 83.49 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 | 292 | IMAGE PLATE | MARRESEARCH | MIRRORS | 1997-07-23 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH2R |
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 | 2.5 | 20 | 99.8 | 0.12 | 0.12 | 9 | 7.4 | 6058 | 1 |
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) | ||||||||||
2.5 | 2.57 | 67.1 | 0.53 | 0.53 | 5.1 | 7.3 |
Refinement
Statistics | |||||||||||||||||||
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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 | DIFFERENCE FOURIER | THROUGHOUT | PDB ENTRY 1SBG | 2.8 | 20 | 4054 | 412 | 95.6 | 0.201 | 0.201 | 0.255 | RANDOM | 17.5 |
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] | |
17.5 | 17.5 | 17.5 | 17.5 | 17.5 | 17.5 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 29.2 |
x_angle_deg | 3.4 |
x_improper_angle_d | 1.8 |
x_bond_d | 0.019 |
x_bond_d_na | |
x_bond_d_prot | |
x_angle_d | |
x_angle_d_na | |
x_angle_d_prot | |
x_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1502 |
Nucleic Acid Atoms | |
Solvent Atoms | 4 |
Heterogen Atoms | 78 |
Software
Software | |
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Software Name | Purpose |
X-PLOR | model building |
X-PLOR | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
X-PLOR | phasing |