3O9B
Crystal Structure of wild-type HIV-1 Protease in Complex with kd25
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1F7A | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | hanging drop, vapor diffusion | 6.2 | 295 | 126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 24-29% Ammonium Sulfate, hanging drop, vapor diffusion, temperature 295K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.09 | 41.27 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 50.672 | ¦Á = 90 |
| b = 57.921 | ¦Â = 90 |
| c = 61.746 | ¦Ã = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
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 QUANTUM 315 | 2009-04-16 | SINGLE WAVELENGTH | |||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 14-BM-C | 0.9 | APS | 14-BM-C |
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 | 1.5 | 50 | 99.8 | 0.067 | 11.7 | 7.8 | 29830 | ||||||||||||
| 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 | 1.5 | 1.55 | 100 | 0.368 | 7.9 | ||||||||||||||
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 ? | 1.5 | 42.26 | 28263 | 1508 | 99.82 | 0.16637 | 0.16521 | 0.18898 | RANDOM | 11.433 | ||||||
| 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] | |
| -0.63 | 0.21 | 0.41 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 42.284 |
| r_dihedral_angle_4_deg | 11.586 |
| r_dihedral_angle_3_deg | 11.354 |
| r_dihedral_angle_1_deg | 6.135 |
| r_scangle_it | 2.332 |
| r_scbond_it | 1.499 |
| r_angle_refined_deg | 1.266 |
| r_mcangle_it | 0.92 |
| r_angle_other_deg | 0.778 |
| r_mcbond_it | 0.489 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1498 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 168 |
| Heterogen Atoms | 69 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| AMoRE | phasing |
