Joint X-ray/neutron structure of HIV-1 protease triple mutant (V32I,I47V,V82I) with darunavir at pH 6.0
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 |
|---|
| 2.82 | 56.41 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 59.724 | α = 90 |
| b = 87.257 | β = 90 |
| c = 46.547 | 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 | 2014-08-20 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 293 | IMAGE PLATE | MAATEL IMAGINE | COLLIMATORS | 2014-10-13 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.540 | | |
| 2 | NUCLEAR REACTOR | LADI/ILL | 2.80 - 4.0 | | |
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 | 1.85 | 40 | 98.2 | 0.048 | | | | | | 26.5 | 3.9 | | 21102 | | | |
| 2 | 2 | 27.61 | 83.5 | 0.147 | | | | | | 5.2 | 5.9 | | 13170 | | | |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1.85 | 1.92 | | 0.478 | | | | | | 2.8 | 3.9 | |
| 2 | 2 | 2.11 | | 0.267 | | | | | | 3.2 | 5.2 | |
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 | 1.85 | 20 | | 2.5 | 21426 | 18339 | 926 | 87.9 | | | 0.194 | 0.18 | 0.201 | 0.19 | RANDOM | 27.3 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2 | 40 | | 2.5 | 16128 | 11729 | 564 | 68.8 | | | 0.217 | | 0.245 | | RANDOM | 27.3 |
| 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 |
|---|
| c_torsion_deg | 16.4 |
| c_torsion_deg | 16.4 |
| c_angle_deg | 1 |
| c_angle_deg | 1 |
| c_torsion_impr_deg | 0.85 |
| c_torsion_impr_deg | 0.85 |
| c_bond_d | 0.008 |
| c_bond_d | 0.008 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1514 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 116 |
| 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 |
