7N6T
Crystal structure of inhibitor-free HIV-1 PRS17 revertant mutant PRS17 V48G
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4Z4X | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | 0.2 M sodium citrate tribasic dihydrate, 0.1 M HEPES pH 7.5, 20% w/v 2-propanol |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.5 | 50.84 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 45.34 | α = 90 |
| b = 45.34 | β = 90 |
| c = 105.093 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 41 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 16M | 2020-02-22 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.0 | APS | 22-ID |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (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 | 1.32 | 50 | 97.6 | 0.056 | 0.064 | 0.029 | 15.5 | 4.7 | 48738 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 1.32 | 1.37 | 86.1 | 0.528 | 0.614 | 0.306 | 0.877 | 3.3 | |||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4z4x | 1.32 | 34.35 | 46202 | 2486 | 97.5 | 0.1592 | 0.1577 | 0.186 | RANDOM | 23.991 | ||||||
| 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] | |
| -1.19 | -1.19 | 2.38 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.808 |
| r_dihedral_angle_4_deg | 17.878 |
| r_rigid_bond_restr | 11.507 |
| r_dihedral_angle_3_deg | 10.846 |
| r_dihedral_angle_1_deg | 6.797 |
| r_angle_refined_deg | 2.194 |
| r_angle_other_deg | 1.587 |
| r_chiral_restr | 0.119 |
| r_bond_refined_d | 0.019 |
| r_gen_planes_refined | 0.014 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1516 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 161 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| HKL-2000 | data scaling |
| PHASER | phasing |
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
