HIV Integrase core domain in complex with inhibitor 2-(2-ethynyl-5-methyl-1-benzofuran-3-yl)acetic acid
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 293 | 2.2 M ammonium sulfate, 100 mM potassium iodide | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.06 | 40.37 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 46.029 | α = 90 |
| b = 46.029 | β = 90 |
| c = 139.457 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 21 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 Capillaries | 2015-01-27 | 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 | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 2.19 | 43.71 | 97.2 | 0.053 | 0.059 | 0.026 | 0.999 | 27.6 | 4.5 | 8268 | 28.304 | ||||||||
| 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 | 2.19 | 2.26 | 0.292 | 0.341 | 0.171 | 0.883 | 5.5 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | 2.19 | 43.71 | 7175 | 771 | 96.12 | 0.21671 | 0.21109 | 0.22 | 0.26956 | 0.27 | RANDOM | 35.108 | |||||
| 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] | |
| 0.66 | 0.66 | -1.31 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 29.397 |
| r_dihedral_angle_3_deg | 19.367 |
| r_dihedral_angle_4_deg | 17.295 |
| r_dihedral_angle_1_deg | 9.406 |
| r_long_range_B_refined | 7.457 |
| r_long_range_B_other | 7.439 |
| r_scangle_other | 4.542 |
| r_mcangle_it | 3.875 |
| r_mcangle_other | 3.874 |
| r_scbond_it | 2.775 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1062 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 26 |
| Heterogen Atoms | 26 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| Aimless | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
