3AVF
Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF binding site
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 40mM Tris pH 8.0, 250mM NaCl, 30mM MgCl2, 5mM DTT, 1.6-2.0M ammonium sulfate, 100mM sodium acetate buffer pH 5.0-5.5, vapor diffusion, sitting drop, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.34 | 47.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 70.653 | α = 90 |
b = 70.653 | β = 90 |
c = 66.862 | γ = 120 |
Symmetry | |
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Space Group | P 31 |
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 315 | 2009-12-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.96 | Australian Synchrotron | MX2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 66.9 | 41088 | 41088 |
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 | 1.7 | 61.19 | 41063 | 2065 | 99.96 | 0.1629 | 0.161 | 0.1994 | RANDOM | 21.9638 |
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] | |
0.15 | 0.08 | 0.15 | -0.23 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.035 |
r_dihedral_angle_3_deg | 15.981 |
r_dihedral_angle_4_deg | 8.817 |
r_dihedral_angle_1_deg | 6.077 |
r_angle_refined_deg | 2.631 |
r_chiral_restr | 0.213 |
r_bond_refined_d | 0.031 |
r_gen_planes_refined | 0.014 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2453 |
Nucleic Acid Atoms | |
Solvent Atoms | 169 |
Heterogen Atoms | 54 |
Software
Software | |
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Software Name | Purpose |
d*TREK | data scaling |
SCALA | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
d*TREK | data reduction |