Crystal Structure of Nelfinavir-Resistant, Inactive HIV-1 Protease (D30N/N88D) in Complex with the p1-p6 substrate variant (L449F/S451N)
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1T3R | PDB entry 1T3R |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 295 | 24% PEG 5000, 0.3M ammonium sulfate, 0.5M MES monohydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.97 | 37.55 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 51.474 | α = 90 |
| b = 59.545 | β = 98.6 |
| c = 59.362 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
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 | MAR CCD 165 mm | Mirrors | 2009-03-09 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 14-ID-B | 1.033 | APS | 14-ID-B |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.68 | 50 | 98.8 | 0.064 | 16.85 | 3.8 | 39171 | 2 | |||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1T3R | 1.9 | 40 | 26425 | 1412 | 98.86 | 0.19905 | 0.19638 | 0.2 | 0.24797 | 0.25 | RANDOM | 30.998 | ||||
| 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] | |
| -3.24 | -0.21 | 1.02 | 2.18 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 42.266 |
| r_dihedral_angle_4_deg | 16.702 |
| r_dihedral_angle_3_deg | 13.977 |
| r_dihedral_angle_1_deg | 7.358 |
| r_mcangle_it | 4.382 |
| r_scbond_it | 3.801 |
| r_mcbond_other | 3.216 |
| r_mcbond_it | 3.215 |
| r_angle_refined_deg | 1.534 |
| r_angle_other_deg | 0.726 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3053 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 83 |
| Heterogen Atoms | 18 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| BioCARS-developed | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
