6W42
HIV Integrase core domain in complex with inhibitor 2-(5-methyl-2-(2-(thiophen-2-yl)ethynyl)-1-benzofuran-3-yl)acetic acid
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 2.2 M ammonium sulfate, 100 mM potassium iodide |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.06 | 40.22 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.18 | α = 90 |
b = 46.18 | β = 90 |
c = 139.43 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 | IMAGE PLATE | RIGAKU RAXIS IV++ | AXCO Capillary optics | 2015-03-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.26 | 32.76 | 100 | 0.05 | 0.057 | 0.027 | 0.998 | 15.3 | 4.4 | 7718 | 32.2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.26 | 2.33 | 0.181 | 0.207 | 0.1 | 0.987 | 7.1 |
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 | FOURIER SYNTHESIS | THROUGHOUT | 2.26 | 32.78 | 6828 | 837 | 99.77 | 0.21406 | 0.20843 | 0.25932 | RANDOM | 39.888 |
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] | |
0.14 | 0.14 | -0.29 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.857 |
r_dihedral_angle_4_deg | 30.373 |
r_dihedral_angle_3_deg | 19.462 |
r_dihedral_angle_1_deg | 8.545 |
r_long_range_B_refined | 7.536 |
r_long_range_B_other | 7.534 |
r_scangle_other | 4.839 |
r_mcangle_it | 3.728 |
r_mcangle_other | 3.725 |
r_scbond_it | 3.076 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1066 |
Nucleic Acid Atoms | |
Solvent Atoms | 25 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data reduction |
Aimless | data scaling |
REFMAC | phasing |