3DS4
HIV-1 capsid C-terminal domain mutant (L211S) 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 | PDB entry 2BUO |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 298 | PEG4000, 200mM ammonium sulfate, EVAPORATION, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 44.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 31.51 | α = 90 |
b = 69.27 | β = 97.66 |
c = 41.55 | 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 | MARMOSAIC 225 mm CCD | 2007-03-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 1.0080 | ESRF | ID23-1 |
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 | 1.12 | 41.2 | 93.2 | 0.048 | 0.048 | 14.4 | 3.8 | 63254 |
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) | ||||||||||
1.12 | 1.19 | 73.3 | 0.41 | 0.41 | 2.4 | 5.6 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 2BUO | 1.12 | 35.4 | 62969 | 2022 | 95.84 | 0.20907 | 0.20827 | 0.23412 | RANDOM | 17.054 |
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] | |
0.01 | -0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.83 |
r_dihedral_angle_4_deg | 14.197 |
r_dihedral_angle_3_deg | 11.544 |
r_dihedral_angle_1_deg | 4.238 |
r_scangle_it | 2.65 |
r_sphericity_free | 2.49 |
r_scbond_it | 2.256 |
r_sphericity_bonded | 2.135 |
r_rigid_bond_restr | 1.994 |
r_mcangle_it | 1.364 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1303 |
Nucleic Acid Atoms | |
Solvent Atoms | 321 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
RemDAq | data collection |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |