Joint neutron and X-ray structure of per-deuterated HIV-1 protease in complex with clinical inhibitor amprenavir
NEUTRON DIFFRACTION - X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | 6 | 290 | 0.1M MES, pH=6; 0.8M NaCl, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.79 | 55.99 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 59.186 | α = 90 |
| b = 87.431 | β = 90 |
| c = 46.405 | 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++ | RIGAKU OSMIC VariMax | 2012-11-01 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 293 | IMAGE PLATE | MAATEL CYLINDRICAL | SET OF COLLIMATORS | 2012-10-02 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54 | | IN-HOUSE |
| 2 | NUCLEAR REACTOR | OTHER | 2.8-4.0 | | LADI-III |
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 | 2 | 59.11 | 50.9 | 0.128 | | | | | | 7.5 | 3.2 | | 12800 | | | |
| 2 | 2 | 40 | 94.9 | 0.074 | | | | | | 36.3 | 7.1 | | 16006 | | | |
| 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 | 2 | 2.11 | | 0.269 | | | | | | 4.1 | 3.1 | |
| 2 | 2 | 2.07 | | 0.494 | | | | | | 4.9 | 6.6 | |
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 | 2.01 | 19.77 | | | 16681 | 14719 | 724 | 88.2 | | | 0.194 | | 0.203 | | random | 30.53 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2 | 20 | | 3 | | 12800 | 565 | 77.3 | | 0.244 | 0.244 | | 0.261 | | random | 30.53 |
| 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 | 17.2 |
| x_torsion_deg | 17.2 |
| x_angle_deg | 1 |
| x_angle_deg | 1 |
| x_torsion_impr_deg | 0.88 |
| x_torsion_impr_deg | 0.88 |
| x_bond_d | 0.008 |
| x_bond_d | 0.008 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1512 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 131 |
| Heterogen Atoms | 36 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| nCNS | refinement |
| MAATEL | data collection |
| LAUEGEN | data reduction |
| LSCALE | data scaling |
| CNS | phasing |
