Structure of lysozyme obtained on SSRF using serial synchrotron crystallography
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 193L | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | MICROBATCH | | 293 | sodium chloride, PEG20000 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.07 | 40.54 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 79 | α = 90 |
| b = 79 | β = 90 |
| c = 38 | 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 | 298 | PIXEL | DECTRIS PILATUS3 S 6M | | 2020-11-20 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | SSRF BEAMLINE BL18U1 | 0.98 | SSRF | BL18U1 |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | | fixed target |
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 | 2.15 | 34.25 | 99.26 | 0.885 | 0.2752 | 3.98 | 14.17 | | 6887 | | | 77.29 |
| 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 | 2.15 | 2.23 | | | 0.577 | 0.5341 | 2.45 | | |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 193L | 2.15 | 34.244 | 6887 | 687 | 99.26 | 0.1887 | 0.1874 | 0.19 | 0.2 | 0.2 | 77.2344 |
| 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 | 13.98 |
| f_angle_d | 1.149 |
| f_chiral_restr | 0.048 |
| f_bond_d | 0.009 |
| f_plane_restr | 0.004 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1000 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 48 |
| Heterogen Atoms | 2 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| CrystFEL | data reduction |
| CrystFEL | data scaling |
| PHENIX | phasing |
