SFX crystal structure of hen egg-white lysozyme (HEWL) using a guanosine derivative hydrogel as crystal matrix
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 7BHK | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | BATCH MODE | 4.6 | 293.15 | 0,5 M Na-Acetate, 18 % w/v NaCl, 6 % w/v PEG 6K, pH 4.6 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.11 | 41.62 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 78.8 | α = 90 |
| b = 78.8 | β = 90 |
| c = 38.9 | 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 | 293.15 | CCD | MPCCD | | 2022-11-01 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | FREE ELECTRON LASER | SACLA BEAMLINE BL2 | 1.5498 | SACLA | BL2 |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | Guanosine hydrogel as matrix | injection |
| Measurement |
|---|
| Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
|---|
| 1 | 10 (fs) | 30 | 2.24 | 8000 (KeV) | |
| Data Reduction |
|---|
| Diffraction ID | Frames Indexed | Crystal Hits | Frames Indexed | Latices Merged |
|---|
| 1 | | 22150 | | |
| Injection |
|---|
| Diffraction ID | Description | Flow Rate | Injector Diameter | Injection Power | Injector Nozzle | Filter Size | Carrier Solvent |
|---|
| 1 | HVE | undefined (µl/min) | undefined (µm) | | | | G4 (guanosine hydrogel) |
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 | 1.75 | 39.9 | 100 | 0.991 | 0.0754 | 0.113 | 792.3 | | 13213 | | | 39.3 |
| 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 | 1.75 | 1.79 | 100 | | 0.576 | 0.83 | 1.02 | 117.2 | |
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 | 1.75 | 27.86 | 1.35 | 12847 | 627 | 99.99 | 0.1976 | 0.1963 | 0.1969 | 0.2204 | 0.221 | 26.79 |
| 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 | 12.2131 |
| f_angle_d | 0.9737 |
| f_chiral_restr | 0.0641 |
| f_plane_restr | 0.0094 |
| f_bond_d | 0.0089 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 987 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 103 |
| Heterogen Atoms | |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| CrystFEL | data collection |
| PHENIX | refinement |
