3VQ5
HIV-1 IN core domain in complex with N-METHYL-1-(4-METHYL-2-PHENYL-1,3-THIAZOL-5-YL)METHANAMINE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3L3U | PDB ENTRY 3l3u |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 295 | 1.6M AmSO4, 0.1M Na Citrate pH 4.6, 50mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 41.41 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 49.13 | ¦Á = 90 |
b = 49.13 | ¦Â = 90 |
c = 103.05 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 32 |
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 315r | Mirror | 2009-05-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.979461 | Australian Synchrotron | MX2 |
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 | 1.7 | 50 | 99.6 | 0.059 | 0.058 | 19.55 | 5.6 | 30488 |
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 | 1.7 | 1.75 | 99.8 | 0.319 | 0.422 | 5.06 | 5.6 | 2553 |
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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 3l3u | 1.7 | 42.55 | 30492 | 28963 | 1525 | 99.61 | 0.1918 | 0.17948 | 0.17772 | 0.21321 | RANDOM | 28.336 |
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] | |
1.02 | 0.51 | 1.02 | -1.54 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.981 |
r_dihedral_angle_4_deg | 19.174 |
r_dihedral_angle_3_deg | 15.485 |
r_dihedral_angle_1_deg | 6.428 |
r_angle_refined_deg | 2.185 |
r_chiral_restr | 0.162 |
r_bond_refined_d | 0.021 |
r_gen_planes_refined | 0.013 |
r_bond_other_d | |
r_angle_other_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2041 |
Nucleic Acid Atoms | |
Solvent Atoms | 106 |
Heterogen Atoms | 66 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
AMoRE | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |