Room temperature structure of HIV-1 Integrase catalytic core domain by serial femtosecond crystallography.
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 1ITG | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | BATCH MODE | | 289 | 0.2mM Ammonium sulfate,
0.1M sodiumcacodylate trihydrate,
30% PEG 8000 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.9 | 62.82 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 73.275 | α = 90 |
| b = 73.275 | β = 90 |
| c = 66.71 | γ = 120 |
| Symmetry |
|---|
| Space Group | P 31 2 1 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 298 | CCD | RAYONIX MX-225 | | 2018-10-15 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | FREE ELECTRON LASER | PAL-XFEL BEAMLINE NCI | 0.987 | PAL-XFEL | NCI |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | | injection |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.5 | 24.67 | 99.85 | 0.9935 | 0.09 | 7.26 | 406.99 | | 13866 | | | |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 2.5 | 2.61 | 100 | | 0.5506 | 0.7737 | 1.45 | 275.68 | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1ITG | 2.5 | 24.665 | 1.34 | 7450 | 771 | 99.99 | 0.1802 | 0.1766 | 0.18 | 0.2117 | 0.21 | |
| 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 |
|---|
| f_dihedral_angle_d | 11.981 |
| f_angle_d | 0.446 |
| f_chiral_restr | 0.041 |
| f_bond_d | 0.003 |
| f_plane_restr | 0.003 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1098 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 12 |
| Heterogen Atoms | 8 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| Coot | model building |
| PHASER | phasing |
| CrystFEL | data scaling |
| Cheetah | data reduction |
