Crystal structure of hen egg white lysozyme using drop-on-drop SFX method - 0.2 s mixing with N-acetyl-D-glucosamine.
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 4ETA | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | BATCH MODE | | 295 | 1 M citric acid, 20% (w/v) NaCl, 5% (w/v) PEG 6000, pH 3.0 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.06 | 40.25 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 78.804 | α = 90 |
| b = 78.804 | β = 90 |
| c = 38.002 | 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 | 308 | CCD | RAYONIX MX300-HS | | 2019-07-11 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | FREE ELECTRON LASER | SACLA BEAMLINE BL2 | 1.24 | SACLA | BL2 |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | acoustic droplet ejection | injection |
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 | 1.45 | 55.72 | 100 | 0.94 | 0.2 | 55.75 | 52.84 | | 21782 | | | 23.47 |
| 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 | 1.45 | 1.475 | 100 | | 0.03 | 0.129 | 0.497 | | |
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 | FREE R-VALUE | 4ETA | 1.45 | 34.23 | 1.33 | 21663 | 1076 | 99.46 | 0.1978 | 0.197 | 0.2 | 0.2108 | 0.21 | 27.4 |
| 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 | 11.8211 |
| f_angle_d | 0.7572 |
| f_chiral_restr | 0.0779 |
| f_bond_d | 0.0051 |
| f_plane_restr | 0.004 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 990 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 79 |
| Heterogen Atoms | 5 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| cctbx.xfel | data processing |
| PHASER | phasing |
| PHENIX | refinement |
