Serial synchrotron in plate room temperature structure of Dye Type Peroxidase Aa
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 6I43 | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | BATCH MODE | 7 | 291 | 1:3 v/v ratio of 10 mg/ml protein in 20 mM sodium phosphate, 150 mM NaCl, pH 7.0 and a mother liquor solution (12% v/v PEG 3350, 100 mM HEPES pH 7.0) |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.2 | 43.97 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 72.474 | α = 90 |
| b = 67.765 | β = 105.7 |
| c = 74.733 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 1 21 1 |
|---|
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 | DECTRIS EIGER2 X 4M | | 2023-10-04 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | DIAMOND BEAMLINE VMXi | 0.775 | Diamond | VMXi |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | In Plate | fixed target |
| Fixed Target |
|---|
| Diffraction ID | Description | Sample Holding | Support Base | Motion control | Details | Sample Solvent |
|---|
| 1 | Mitegen in situ-1 plate | | | | | |
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 | 1.79 | 69.77 | 99.75 | 0.99 | 0.121 | 21.8 | 98.9 | | 65821 | | | 22 |
| 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 | 1.79 | 1.854 | | | 0.315 | 0.978 | | | |
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 | R-Free | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.79 | 69.77 | 1.34 | 65657 | 1946 | 99.75 | 0.1898 | 0.1886 | 0.2281 | 23.16 |
| 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 | 15.2563 |
| f_angle_d | 1.0531 |
| f_chiral_restr | 0.0609 |
| f_plane_restr | 0.0135 |
| f_bond_d | 0.0087 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 5503 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 416 |
| Heterogen Atoms | 86 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| Coot | model building |
| xia2 | data reduction |
| xia2 | data scaling |
| PHENIX | phasing |
