3VQ7
HIV-1 IN core domain in complex with 4-(1H-pyrrol-1-yl)aniline
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 | 5.6 | 295 | 1.6M AmSO4, 0.1M Na Citrate pH 5.6, 50mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.21 | 44.33 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.284 | α = 90 |
b = 61.658 | β = 90 |
c = 82.017 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 210r | Mirror | 2007-09-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX1 | 0.95363 | Australian Synchrotron | MX1 |
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 | 34.15 | 99.57 | 0.08 | 0.09 | 15.2 | 7.2 | 38588 | 38422 | 2 | 2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.634 | 1.692 | 95.74 |
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 | 1.63 | 34.15 | 38588 | 36498 | 1924 | 99.46 | 0.199 | 0.20042 | 0.199 | 0.22677 | RANDOM | 20.482 |
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] | |
-0.33 | 1.43 | -1.1 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.937 |
r_dihedral_angle_3_deg | 14.657 |
r_dihedral_angle_4_deg | 13.073 |
r_dihedral_angle_1_deg | 5.987 |
r_scangle_it | 3.293 |
r_scbond_it | 2.293 |
r_angle_refined_deg | 1.749 |
r_mcangle_it | 1.715 |
r_mcbond_it | 1.202 |
r_angle_other_deg | 0.959 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2190 |
Nucleic Acid Atoms | |
Solvent Atoms | 118 |
Heterogen Atoms | 61 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
AMoRE | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |