Dark state SFX structure of hen egg white lysozyme microcrystals immobilized with a Mn carbonyl complex at RT.
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 | BATCH MODE | 3 | 293 | 0.1M Acetate buffer (pH3.0), 28% NaCl |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.17 | 43.33 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 81 | α = 90 |
| b = 81 | β = 90 |
| c = 37.7 | 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 | CCD | MPCCD | | 2020-11-24 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | FREE ELECTRON LASER | SACLA BEAMLINE BL2 | 1 | SACLA | BL2 |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | | injection |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | 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 | 1.6 | 31.49 | 100 | 0.9649 | 6.82 | 448.21 | | 17136 | | | 19.64 |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 1.6 | 1.62 | | | 0.9057 | | | |
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 | 1.6 | 31.49 | 1.34 | 17095 | 855 | 100 | 0.195 | 0.1934 | 0.19 | 0.2263 | 0.22 | 22.5 |
| 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 | 6.842 |
| f_angle_d | 0.9398 |
| f_chiral_restr | 0.0572 |
| f_plane_restr | 0.0261 |
| f_bond_d | 0.0066 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 995 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 86 |
| Heterogen Atoms | 9 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| Cheetah | data collection |
| CrystFEL | data reduction |
| PHASER | phasing |
| PHENIX | refinement |
| Coot | model building |
