Joint X-ray/neutron structure of HIV-1 protease triple mutant (V32I,I47V,V82I) with darunavir at pH 4.3
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 4JEC | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | | 291 | NaCl, MES |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.81 | 56.19 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 59.593 | α = 90 |
| b = 87.428 | β = 90 |
| c = 46.328 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 21 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 | 293 | IMAGE PLATE | RIGAKU RAXIS IV++ | OSMIC VARIMAX | 2014-11-08 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 293 | IMAGE PLATE | MAATEL IMAGINE | ELLIPTICAL MIRRORS | 2014-12-04 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.540 | | |
| 2 | NUCLEAR REACTOR | ORNL High Flux Isotope Reactor BEAMLINE CG4D | 2.8-4.0 | ORNL High Flux Isotope Reactor | CG4D |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | 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 | 1.75 | 40 | 86.2 | | | | | | | 34 | 4.3 | | 21726 | | | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | 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 | 1.75 | 33.74 | | | 25099 | 19201 | 949 | 76.5 | | | 0.203 | 0.19 | 0.218 | 0.21 | | 27.64 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.3 | 36.58 | | | 11249 | 7848 | 337 | 69.8 | | | 0.212 | | 0.224 | | | 27.64 |
| 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] |
|---|
| | | | | |
| | | | | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| x_torsion_deg | 18.9 |
| x_torsion_deg | 18.9 |
| x_angle_deg | 1.1 |
| x_angle_deg | 1.1 |
| x_torsion_impr_deg | 0.96 |
| x_torsion_impr_deg | 0.96 |
| x_bond_d | 0.009 |
| x_bond_d | 0.009 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1514 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 105 |
| Heterogen Atoms | 38 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| PHASER | phasing |
| nCNS | refinement |
| LAUEGEN | data reduction |
| LSCALE | data scaling |
