Crystal structure of lysozyme by fixed-target serial femtosecond crystallography
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 6IG6 | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | SMALL TUBES | 4.5 | 293.5 | sodium acetate, PEG 8000, NaCl |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.02 | 38.96 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 78.22 | α = 90 |
| b = 78.22 | β = 90 |
| c = 37.76 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 43 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 | 296 | CCD | RAYONIX MX225-HS | KB mirror | 2018-10-29 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | FREE ELECTRON LASER | PAL-XFEL BEAMLINE CSI | 1.2782 | PAL-XFEL | CSI |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | fixed target | fixed target |
| Fixed Target |
|---|
| Diffraction ID | Description | Sample Holding | Support Base | Motion control | Details | Sample Solvent |
|---|
| 1 | | mesh | | | | |
| Measurement |
|---|
| Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
|---|
| 1 | 20 (fs) | 30 | 4 | 9700 (KeV) | |
| Data Reduction |
|---|
| Diffraction ID | Frames Indexed | Crystal Hits | Frames Indexed | Latices Merged |
|---|
| 1 | | | | |
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 | 1.65 | 80 | 100 | 0.985 | 0.1028 | 6.61 | 4660.8 | | 29127 | | | |
| 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 | 1.65 | 1.71 | 100 | | 0.37 | 0.7873 | 1.36 | 962.2 | |
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 | 6IG6 | 1.65 | 55.31 | 1.34 | 26937 | 2557 | 99.98 | 0.2069 | 0.2046 | 0.2 | 0.2286 | 0.23 | 44.4569 |
| 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 | 1001 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 42 |
| Heterogen Atoms | 3 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| PHASER | phasing |
| PDB_EXTRACT | data extraction |
| CrystFEL | data reduction |
| CrystFEL | data scaling |
