8QUB
Hexameric HIV-1 CA in complex with DDD00074110
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5HGM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 290 | 0.1M Tris buffer, pH 8.0 to 9.0, 10-15% PEG550MME, 0.15M KSCN |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.66 | 53.73 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 90.84 | α = 90 |
b = 90.84 | β = 90 |
c = 56.83 | γ = 120 |
Symmetry | |
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Space Group | P 6 |
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 | PIXEL | DECTRIS EIGER2 XE 16M | 2016-07-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.976 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 1.63 | 46.07 | 100 | 0.06 | 0.99 | 19.2 | 9.8 | 33459 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.63 | 1.66 | 100 | 1.29 | 0.56 | 8.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.63 | 46.07 | 31848 | 1609 | 99.96 | 0.19063 | 0.18961 | 0.2103 | RANDOM | 32.411 |
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] | |
0.22 | 0.11 | 0.22 | -0.72 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.149 |
r_dihedral_angle_4_deg | 20.591 |
r_dihedral_angle_3_deg | 14.27 |
r_long_range_B_refined | 7.395 |
r_long_range_B_other | 7.313 |
r_scangle_other | 6.263 |
r_dihedral_angle_1_deg | 6.119 |
r_mcangle_it | 4.458 |
r_mcangle_other | 4.456 |
r_scbond_it | 4.322 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1661 |
Nucleic Acid Atoms | |
Solvent Atoms | 191 |
Heterogen Atoms | 17 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
xia2 | data scaling |
MOLREP | phasing |