Joint X-ray/neutron structure of HIV-1 protease triple mutant (V32I,I47V,V82I) with amprenavir at pH 6.0
NEUTRON DIFFRACTION - X-RAY 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 | | 290 | 1M NaCl, 0.1 M NaMES |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.8 | 56.08 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 59.234 | α = 90 |
| b = 87.359 | β = 90 |
| c = 46.565 | 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 | 2016-03-03 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 293 | IMAGE PLATE | MAATEL IMAGINE | COLLIMATORS | 2016-02-22 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54 | | |
| 2 | NUCLEAR REACTOR | LADI/ILL | 2.8-4.0 | | LADI |
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 | 95.9 | 0.046 | | | | | | 26.1 | 4 | | 20505 | | | |
| 2 | 2.2 | 40 | 74.4 | 0.167 | | | | | | 7.2 | 3.9 | | 8933 | | | |
| 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 | 1.85 | 1.92 | | 0.465 | | | | | | 2.7 | 4.1 | |
| 2 | 2.2 | 2.32 | | 0.308 | | | | | | 4 | 3.4 | |
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 | 36.61 | | 2.5 | 21283 | 18040 | 885 | 84.8 | | | 0.191 | | 0.214 | | RANDOM | 27.93 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.2 | 33.76 | | 2.5 | 12268 | 8394 | 397 | 65.6 | | | 0.217 | | 0.255 | | RANDOM | 27.93 |
| 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 | 15.3 |
| x_torsion_deg | 15.3 |
| x_angle_deg | 1.1 |
| x_angle_deg | 1.1 |
| x_torsion_impr_deg | 0.87 |
| x_torsion_impr_deg | 0.87 |
| 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 | 124 |
| Heterogen Atoms | 35 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| PHASER | phasing |
| nCNS | refinement |
| LAUEGEN | data reduction |
| LSCALE | data scaling |
