3TOG
HIV-1 Protease - Epoxydic Inhibitor Complex (pH 9 - Monoclinic Crystal form P21)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2AVV | PDB ENTRY 2AVV |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 9 | 298 | Ammonium sulfate 40%, DMSO 10%, sodium citrate 0.25M. pH has been increased through ammonia diffusion, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.78 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.191 | α = 90 |
b = 62.136 | β = 98.73 |
c = 58.751 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | MAR CCD 165 mm | MIRRORS | 2008-06-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ELETTRA BEAMLINE 5.2R | 1.2 | ELETTRA | 5.2R |
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 | 1.24 | 8.49 | 98 | 0.057 | 10.1 | 2 | 100510 | 2 | 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 | 1.24 | 1.31 | 96.9 | 0.469 | 1.8 | 2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | FOURIER SYNTHESIS | THROUGHOUT | PDB ENTRY 2AVV | 1.24 | 8.49 | 2 | 98016 | 2493 | 97.96 | 0.24287 | 0.24219 | 0.26978 | RANDOM | 14.909 |
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] | |
-0.04 | 0.01 | 0.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.945 |
r_dihedral_angle_4_deg | 17.914 |
r_dihedral_angle_3_deg | 14.315 |
r_dihedral_angle_1_deg | 6.762 |
r_scangle_it | 5.302 |
r_scbond_it | 3.432 |
r_angle_refined_deg | 2.263 |
r_mcangle_it | 2.254 |
r_mcbond_it | 1.409 |
r_chiral_restr | 0.153 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3024 |
Nucleic Acid Atoms | |
Solvent Atoms | 269 |
Heterogen Atoms | 90 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |