SFX structure of dye-type peroxidase DtpB D152A variant in the ferryl state
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 6YRJ | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | BATCH MODE | 7.5 | 293 | 6.2 mg/mL of protein in 20mM Sodium phosphate, 125mM NaCl pH 7 mixed with 125 mM MgCl2, 125 mM HEPES, 18% PEG 4000, pH 7.5 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.47 | 50.17 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 86.52 | α = 90 |
| b = 120.9 | β = 90 |
| c = 197.41 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 21 21 21 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 301 | CCD | MPCCD | | 2021-06-12 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | FREE ELECTRON LASER | SACLA BEAMLINE BL2 | 1.127 | SACLA | BL2 |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | high-viscosity cartridge-type injector | injection |
| Measurement |
|---|
| Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
|---|
| 1 | 10 (fs) | | | undefined (KeV) | |
| Injection |
|---|
| Diffraction ID | Description | Flow Rate | Injector Diameter | Injection Power | Injector Nozzle | Filter Size | Carrier Solvent |
|---|
| 1 | | 0.0068 (µl/min) | undefined (µm) | gas | | | hydroxyethyl cellulose |
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 | 1.9 | 36 | 100 | 0.968 | 0.162 | 4.8 | 1510 | | 163211 | | | |
| 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 | 1.9 | 1.93 | | | 0.282 | 0.863 | | | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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) | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 6YRJ | 1.9 | 36 | 155135 | 8066 | 99.98 | 0.1679 | 0.1662 | 0.18 | 0.2007 | 0.2 | RANDOM | 29.268 |
| 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] |
|---|
| 0.09 | | | 0.13 | | -0.21 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_2_deg | 26.566 |
| r_dihedral_angle_4_deg | 17.178 |
| r_dihedral_angle_3_deg | 13.352 |
| r_dihedral_angle_1_deg | 6.68 |
| r_angle_refined_deg | 1.607 |
| r_angle_other_deg | 1.375 |
| r_chiral_restr | 0.072 |
| r_bond_refined_d | 0.01 |
| r_gen_planes_refined | 0.008 |
| r_gen_planes_other | 0.004 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_2_deg | 26.566 |
| r_dihedral_angle_4_deg | 17.178 |
| r_dihedral_angle_3_deg | 13.352 |
| r_dihedral_angle_1_deg | 6.68 |
| r_angle_refined_deg | 1.607 |
| r_angle_other_deg | 1.375 |
| r_chiral_restr | 0.072 |
| r_bond_refined_d | 0.01 |
| r_gen_planes_refined | 0.008 |
| r_gen_planes_other | 0.004 |
| r_bond_other_d | 0.001 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 13904 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 823 |
| Heterogen Atoms | 267 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| CrystFEL | data reduction |
| CrystFEL | data scaling |
| REFMAC | phasing |
