Dye-decolourising peroxidase DtpB (224 kGy)
Serial Crystallography (SX)  
Starting Model(s)
| Initial Refinement Model(s) | 
|---|
| Type | Source | Accession Code | Details | 
|---|
|
experimental model | PDB |  6YRD |   | 
Crystallization
| Crystalization Experiments | 
|---|
| ID | Method | pH | Temperature | Details | 
|---|
| 1 | BATCH MODE | 7.5 | 293 | 6.2 mg/mL of protein in 20 mM NaPi, 150 mM NaCl pH 7 was mixed with 125 mM MgCl2, 125 mM HEPES, 18% PEG 4000 pH 7.5 | 
| Crystal Properties | 
|---|
| Matthews coefficient | Solvent content | 
|---|
| 2.58 | 52.39 | 
Crystal Data
| Unit Cell | 
|---|
| Length ( Å ) | Angle ( ˚ ) | 
|---|
| a = 86.85 | α = 90 | 
| b = 121.896 | β = 90 | 
| c = 199.551 | 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 | 293 | PIXEL | DECTRIS PILATUS 6M |  | 2019-09-19 | M | SINGLE WAVELENGTH | 
| Radiation Source | 
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline | 
|---|
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.9686 | Diamond | I24 | 
Serial Crystallography
| Sample delivery method | 
|---|
| Diffraction ID | Description | Sample Delivery Method | 
|---|
| 1 | silicon chip | fixed target | 
| Fixed Target | 
|---|
| Diffraction ID | Description | Sample Holding | Support Base | Motion control | Details  | Sample Solvent | 
|---|
| 1 |  | silicone chip |  |  |  |  | 
| Measurement | 
|---|
| Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse | 
|---|
| 1 | undefined (fs) |  |  | undefined (KeV) |  | 
| Data Reduction | 
|---|
| Diffraction ID | Frames Indexed | Crystal Hits | Frames Indexed | Latices Merged | 
|---|
| 1 |  | 21858 |  |  | 
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 | 1.92 | 40.11 | 100 | 0.98 | 0.124 | 1.83 | 78.3 |  | 161825 |  |  |  | 
| 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 | 1.92 | 1.97 | 99.8 |  | 0.57 | 0.705 |  | 12.5 |  | 
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | 
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.92 | 40.11 | 153678 | 8044 | 99.97 | 0.2098 | 0.20799 | 0.2126 | 0.24509 | 0.246 | RANDOM | 33.594 | 
| 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] | 
|---|
| 0.02 |  |  | -0.04 |  | 0.01 | 
| RMS Deviations | 
|---|
| Key | Refinement Restraint Deviation | 
|---|
| r_dihedral_angle_3_deg | 15.194 | 
| r_dihedral_angle_2_deg | 15.156 | 
| r_long_range_B_refined | 9.324 | 
| r_long_range_B_other | 9.323 | 
| r_scangle_other | 8.518 | 
| r_dihedral_angle_1_deg | 7.684 | 
| r_mcangle_it | 6.324 | 
| r_mcangle_other | 6.324 | 
| r_scbond_it | 5.958 | 
| r_scbond_other | 5.958 | 
| RMS Deviations | 
|---|
| Key | Refinement Restraint Deviation | 
|---|
| r_dihedral_angle_3_deg | 15.194 | 
| r_dihedral_angle_2_deg | 15.156 | 
| r_long_range_B_refined | 9.324 | 
| r_long_range_B_other | 9.323 | 
| r_scangle_other | 8.518 | 
| r_dihedral_angle_1_deg | 7.684 | 
| r_mcangle_it | 6.324 | 
| r_mcangle_other | 6.324 | 
| r_scbond_it | 5.958 | 
| r_scbond_other | 5.958 | 
| r_mcbond_it | 4.351 | 
| r_mcbond_other | 4.351 | 
| r_angle_refined_deg | 2.57 | 
| r_angle_other_deg | 0.89 | 
| r_chiral_restr | 0.113 | 
| r_bond_refined_d | 0.016 | 
| r_gen_planes_refined | 0.011 | 
| r_gen_planes_other | 0.006 | 
| r_bond_other_d | 0.001 | 
| r_dihedral_angle_4_deg |  | 
| r_nbd_refined |  | 
| r_nbd_other |  | 
| r_nbtor_refined |  | 
| r_nbtor_other |  | 
| r_xyhbond_nbd_refined |  | 
| r_xyhbond_nbd_other |  | 
| r_metal_ion_refined |  | 
| r_metal_ion_other |  | 
| r_symmetry_vdw_refined |  | 
| r_symmetry_vdw_other |  | 
| r_symmetry_hbond_refined |  | 
| r_symmetry_hbond_other |  | 
| r_symmetry_metal_ion_refined |  | 
| r_symmetry_metal_ion_other |  | 
| r_scangle_it |  | 
| r_rigid_bond_restr |  | 
| r_sphericity_free |  | 
| r_sphericity_bonded |  | 
| Non-Hydrogen Atoms Used in Refinement | 
|---|
| Non-Hydrogen Atoms | Number | 
|---|
| Protein Atoms | 13926 | 
| Nucleic Acid Atoms |  | 
| Solvent Atoms | 243 | 
| Heterogen Atoms | 173 | 
Software
| Software | 
|---|
| Software Name | Purpose | 
|---|
| REFMAC | refinement | 
| DIALS | data reduction | 
| DIALS | data scaling | 
| REFMAC | phasing |