SFX structure of dye-type peroxidase DtpB in the ferric state
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
other | | Unpublished |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | BATCH MODE | 7.5 | 291 | 6-10 mg/mL of protein in 50mM Sodium acetate, 150mM NaCl pH 5 mixed with 150 mM mM MgCl2, 150 mM HEPES, 20% PEG 4000, pH 7.5 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.49 | 50.67 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 86 | α = 90 |
| b = 120.4 | β = 90 |
| c = 197.5 | 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 | | 2019-06-26 | 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 | chip fixed target | fixed target |
| Fixed Target |
|---|
| Diffraction ID | Description | Sample Holding | Support Base | Motion control | Details | Sample Solvent |
|---|
| 1 | Silicon chip | | | | 25600 apertures | |
| Measurement |
|---|
| Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
|---|
| 1 | 10 (fs) | 30 | | undefined (KeV) | |
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 | 1.85 | 103 | 100 | 0.976 | 0.136 | 5 | 518 | | 175001 | | | 26.9 |
| 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 | 1.85 | 1.9 | 100 | | 0.569 | 0.678 | | 360 | |
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 | Unpublished | 1.85 | 13 | 172358 | 1982 | 99.62 | 0.1597 | 0.1593 | 0.16 | 0.1916 | 0.19 | RANDOM | 33.503 |
| 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] |
|---|
| 0.24 | | | -0.15 | | -0.09 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_2_deg | 27.167 |
| r_dihedral_angle_4_deg | 17.823 |
| r_dihedral_angle_3_deg | 13.507 |
| r_dihedral_angle_1_deg | 6.934 |
| r_angle_refined_deg | 1.716 |
| r_angle_other_deg | 1.447 |
| r_chiral_restr | 0.077 |
| r_bond_refined_d | 0.012 |
| r_gen_planes_refined | 0.009 |
| r_gen_planes_other | 0.006 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_2_deg | 27.167 |
| r_dihedral_angle_4_deg | 17.823 |
| r_dihedral_angle_3_deg | 13.507 |
| r_dihedral_angle_1_deg | 6.934 |
| r_angle_refined_deg | 1.716 |
| r_angle_other_deg | 1.447 |
| r_chiral_restr | 0.077 |
| r_bond_refined_d | 0.012 |
| r_gen_planes_refined | 0.009 |
| r_gen_planes_other | 0.006 |
| r_bond_other_d | 0.001 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 13922 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 810 |
| Heterogen Atoms | 259 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| CrystFEL | data reduction |
| CrystFEL | data scaling |
| REFMAC | phasing |