4COC
HIV-1 capsid C-terminal domain mutant (Y169L)
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 | 8.5 | 30% PEG 4000, 0.2 M LISO4, 0.1 M TRIS PH 8.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.47 | 50.28 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 100.48 | α = 90 |
b = 33.76 | β = 108.32 |
c = 77.73 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | ONE PAIR OF (300X40X15) MM3 LONG PT COATED SI MIRROR, 260MM USABLE, IN A KIRKPATRICK-BAEZ GEOMETRY | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | ESRF | ID23-2 |
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 | 1.59 | 47.42 | 97.9 | 0.09 | 13.1 | 5.6 | 33062 | 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 | 1.59 | 1.68 | 77.8 | 0.52 | 2 | 2.6 |
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 | 1.59 | 47.42 | 31387 | 1675 | 97.9 | 0.1884 | 0.18656 | 0.22323 | RANDOM | 22.288 |
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] | |
-0.57 | -0.34 | -0.39 | 0.75 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.536 |
r_dihedral_angle_1_deg | 18.101 |
r_dihedral_angle_4_deg | 15.464 |
r_dihedral_angle_3_deg | 13.577 |
r_scangle_it | 7.307 |
r_scbond_it | 4.425 |
r_mcangle_it | 3.196 |
r_angle_refined_deg | 2.642 |
r_mcbond_it | 1.866 |
r_chiral_restr | 0.199 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1775 |
Nucleic Acid Atoms | |
Solvent Atoms | 174 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |