Lysozyme crystal structure by beam sweeping serial crystallography
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 5WRA | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | | 296 | 1M NaCl, 40% (v/v) ethylene glycol, 15% (w/v) PEG4000, 50 mM sodium acetate pH 3.5 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.05 | 39.98 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 79.03 | α = 90 |
| b = 79.03 | β = 90 |
| c = 37.62 | 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 | PSI JUNGFRAU 4M | | 2024-09-23 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | FREE ELECTRON LASER | EUROPEAN XFEL BEAMLINE SPB/SFX | 1.36245 | European XFEL | SPB/SFX |
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 | 35.34 | 99.98 | 0.97 | 0.1037 | 12.39 | 1075.9 | | 8478 | | | 6.3 |
| 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 | 2.13 | 100 | | 0.91 | 0.2066 | 6.31 | 239.6 | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2 | 35.34 | 1.39 | 8478 | 848 | 99.99 | 0.2122 | 0.2073 | 0.2071 | 0.2558 | 0.2558 | 10.62 |
| 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 | 13.078 |
| f_angle_d | 0.9268 |
| f_chiral_restr | 0.052 |
| f_plane_restr | 0.0105 |
| f_bond_d | 0.0074 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1000 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 65 |
| Heterogen Atoms | 1 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| CrystFEL | data reduction |
| CrystFEL | data scaling |
| PHASER | phasing |
