3AO3
Fragment-based approach to the design of ligands targeting a novel site on HIV-1 integrase
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 | 293 | 1.8M AmSO4, 0.15 M Na Citrate pH 4.6, 5 mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.02 | 39.12 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49 | α = 90 |
b = 49 | β = 90 |
c = 103.6 | γ = 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 210r | mirrors | 2008-08-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX1 | 0.957 | 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 | 1.9 | 50 | 96.8 | 0.041 | 0.046 | 26.6 | 5.7 | 21930 | 21222 | 32.6 |
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) | ||||||||||
1.9 | 2 | 91.8 | 0.288 | 0.318 | 6.2 | 5.7 | 2860 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 3l3u | 1.9 | 39.27 | 21222 | 20732 | 1092 | 100 | 0.18122 | 0.17811 | 0.24111 | RANDOM | 29.28 |
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] | |
1.3 | 0.65 | 1.3 | -1.94 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.951 |
r_dihedral_angle_3_deg | 15.482 |
r_dihedral_angle_4_deg | 11.441 |
r_dihedral_angle_1_deg | 6.044 |
r_scangle_it | 5.173 |
r_scbond_it | 3.274 |
r_mcangle_it | 2.604 |
r_angle_refined_deg | 2.075 |
r_mcbond_it | 1.461 |
r_chiral_restr | 0.17 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2087 |
Nucleic Acid Atoms | |
Solvent Atoms | 89 |
Heterogen Atoms | 72 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
AMoRE | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |