4CF8
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 5.5 | THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5. | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.95 | 58 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 70.431 | α = 90 |
| b = 70.431 | β = 90 |
| c = 66.683 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 31 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | CCD | ADSC CCD | 2009-08-05 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX1 | Australian Synchrotron | MX1 | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.65 | 66.7 | 100 | 0.08 | 15.6 | 5.6 | 44559 | 1 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 1.65 | 1.74 | 100 | 0.49 | 2.7 | 5.6 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | PDB ENTRY 3ZSQ | 1.65 | 44.99 | 42283 | 2244 | 99.99 | 0.17657 | 0.17551 | 0.19642 | RANDOM | 21.102 | ||||||
| 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] | |
| 0.11 | 0.11 | 0.11 | -0.37 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 30.282 |
| r_dihedral_angle_3_deg | 13.395 |
| r_dihedral_angle_4_deg | 9.557 |
| r_dihedral_angle_1_deg | 5.157 |
| r_long_range_B_refined | 4.482 |
| r_long_range_B_other | 4.481 |
| r_scangle_other | 2.391 |
| r_mcangle_other | 1.922 |
| r_mcangle_it | 1.921 |
| r_scbond_it | 1.407 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2318 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 145 |
| Heterogen Atoms | 133 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
