2Z4O
Wild Type HIV-1 Protease with potent Antiviral inhibitor GRL-98065
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1FG6 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.8 | 298 | 25mM sodium acetate, 10% (w/v) sodium chloride, 6% dioxane, 10% (v/v) dimethylsulfoxide (DMSO), pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.67 | 53.99 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 58.25 | ¦Á = 90 |
b = 85.832 | ¦Â = 90 |
c = 45.967 | ¦Ã = 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 | doubly focusing toroidal mirror | 2002-11-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X26C | 0.9561 | 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 | 1.6 | 50 | 99.7 | 0.071 | 11 | 5.2 | 31128 | 31020 | 15.3 |
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) | |||||||||||
1.6 | 1.66 | 99.4 | 0.388 | 4.7 | 5.2 | 3029 |
Refinement
Statistics | |||||||||||||||||||
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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 | THROUGHOUT | 1FG6 | 1.6 | 10 | 30875 | 30846 | 1553 | 99.7 | 0.1472 | 0.1438 | 0.2055 | RANDOM |
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] | |
Coordinate Error | ||
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Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
22 | 1631 | 1761.28 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_approx_iso_adps | 0.079 |
s_similar_adp_cmpnt | 0.033 |
s_angle_d | 0.029 |
s_from_restr_planes | 0.0274 |
s_non_zero_chiral_vol | 0.025 |
s_zero_chiral_vol | 0.014 |
s_anti_bump_dis_restr | 0.011 |
s_bond_d | 0.009 |
s_rigid_bond_adp_cmpnt | 0.002 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1605 |
Nucleic Acid Atoms | |
Solvent Atoms | 238 |
Heterogen Atoms | 87 |
Software
Software | |
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Software Name | Purpose |
AMoRE | phasing |
SHELXL-97 | refinement |
ADSC | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |