Light SFX structure of D.m(6-4)photolyase at 1ps time delay
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 8C1U | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | BATCH MODE | 6.5 | 277.15 | 100 mM bis-tris pH=6.5, 200 mM lithium sulphate monohydrate, 22 % PEG 3350, 0.5 % Ethyl acetate. |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.43 | 49.28 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 103.9 | α = 90 |
| b = 103.9 | β = 90 |
| c = 52.19 | γ = 90 |
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 | PIXEL | PSI JUNGFRAU 16M | | 2021-09-27 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | FREE ELECTRON LASER | SwissFEL ARAMIS BEAMLINE ESA | 1 | SwissFEL ARAMIS | ESA |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | | injection |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 1.9 | 15.72 | 100 | 0.09 | 10.97 | 181.74 | | 44138 | | | 5.61 |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 1.9 | 1.91 | | | 0.28 | | | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.9 | 15.72 | 42110 | 2095 | 95.48 | 0.2519 | 0.2509 | 0.2697 | 33.73 |
| 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 | 16.5101 |
| f_angle_d | 0.6434 |
| f_chiral_restr | 0.042 |
| f_plane_restr | 0.0055 |
| f_bond_d | 0.0032 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 4099 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 132 |
| Heterogen Atoms | 59 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| CrystFEL | data reduction |
| CrystFEL | data scaling |
| PHASER | phasing |
