3DS0
HIV-1 capsid C-terminal domain mutant (N183A) in complex with an inhibitor of particle assembly (CAI)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2BUO |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 4.2 | 298 | 32% PEG 4000, 100mM ammonium acetate pH4.2, 10mM MgCl2, EVAPORATION, temperature 298.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.9 | 35.22 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.838 | α = 90 |
b = 42.838 | β = 90 |
c = 90.495 | γ = 90 |
Symmetry | |
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Space Group | P 41 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 | MARMOSAIC 225 mm CCD | Dynamically bendable mirror | 2007-05-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.044 | SLS | X06SA |
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 | 1.6 | 38.7 | 99.4 | 0.079 | 0.079 | 25.6 | 13.9 | 11638 | 22.9 |
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) | ||||||||||
1.6 | 1.66 | 100 | 0.362 | 0.362 | 7.2 | 10.9 | 1140 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2BUO | 1.6 | 38.72 | 11638 | 11086 | 551 | 99.22 | 0.20825 | 0.20636 | 0.24545 | RANDOM | 24.294 |
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] | |
-0.01 | -0.01 | 0.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.649 |
r_dihedral_angle_4_deg | 13.558 |
r_dihedral_angle_3_deg | 11.926 |
r_dihedral_angle_1_deg | 4.528 |
r_scangle_it | 4.069 |
r_sphericity_free | 3.972 |
r_scbond_it | 2.791 |
r_sphericity_bonded | 2.44 |
r_mcangle_it | 1.846 |
r_rigid_bond_restr | 1.705 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 733 |
Nucleic Acid Atoms | |
Solvent Atoms | 78 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
RemDAq | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |