Structure and mutation analysis of the hexameric P4 from Pseudomonas aeruginosa phage phiYY
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 4BLP | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 291 | 600 mM K/Na tartrate, 100 mM Tris-HCl pH 8.5 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.72 | 57.06 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 241.075 | α = 90 |
| b = 241.075 | β = 90 |
| c = 152.95 | γ = 120 |
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 | | 2017-11-23 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | SSRF BEAMLINE BL17U1 | 0.979 | SSRF | BL17U1 |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | | injection |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | 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 | 2.4 | 41.13 | 99.7 | 0.167 | 0.995 | 10.3 | 10.2 | | 242159 | | | |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 2.4 | 2.44 | | | 0.12 | 0.694 | 2.4 | | |
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 | THROUGHOUT | 4blp | 2.45 | 41.13 | 1.96 | 241866 | 12121 | 99.66 | 0.1817 | 0.1803 | 0.18 | 0.2076 | 0.21 | 58.4117 |
| 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] |
|---|
| | | | | |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 15452 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 245 |
| Heterogen Atoms | |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| XDS | data scaling |
| PHENIX | phasing |
