Dye-decolourising peroxidase DtpB mixed with hydrogen peroxide for 6.7 s
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 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 |
|---|
| 2.6 | 52.75 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 86.891 | α = 90 |
| b = 121.661 | β = 90 |
| c = 199.487 | 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 | CCD | RAYONIX MX225-HS | | 2022-06-26 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | FREE ELECTRON LASER | PAL-XFEL BEAMLINE NCI | 1.3042 | PAL-XFEL | NCI |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | | fixed target |
| Fixed Target |
|---|
| Diffraction ID | Description | Sample Holding | Support Base | Motion control | Details | Sample Solvent |
|---|
| 1 | | silicon chip | | | | |
| Measurement |
|---|
| Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
|---|
| 1 | 25 (fs) | | | 9.5 (KeV) | |
| Data Reduction |
|---|
| Diffraction ID | Frames Indexed | Crystal Hits | Frames Indexed | Latices Merged |
|---|
| 1 | | 19553 | | |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | 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 | 1.96 | 58.25 | 100 | 0.999 | 11.1 | 116.3 | | 186481 | | | |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 1.96 | 2.011 | | | 0.25 | | | |
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 | 1.96 | 58.25 | 144425 | 7549 | 99.99 | 0.17012 | 0.16859 | 0.1731 | 0.19977 | 0.2007 | RANDOM | 34.954 |
| 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] |
|---|
| 0.04 | | | 0.14 | | -0.18 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_3_deg | 15.107 |
| r_dihedral_angle_2_deg | 10.481 |
| r_long_range_B_refined | 8.905 |
| r_long_range_B_other | 8.903 |
| r_scangle_other | 7.823 |
| r_dihedral_angle_1_deg | 6.629 |
| r_mcangle_it | 5.772 |
| r_mcangle_other | 5.771 |
| r_scbond_other | 5.571 |
| r_scbond_it | 5.57 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_3_deg | 15.107 |
| r_dihedral_angle_2_deg | 10.481 |
| r_long_range_B_refined | 8.905 |
| r_long_range_B_other | 8.903 |
| r_scangle_other | 7.823 |
| r_dihedral_angle_1_deg | 6.629 |
| r_mcangle_it | 5.772 |
| r_mcangle_other | 5.771 |
| r_scbond_other | 5.571 |
| r_scbond_it | 5.57 |
| r_mcbond_it | 4.456 |
| r_mcbond_other | 4.453 |
| r_angle_refined_deg | 1.766 |
| r_angle_other_deg | 0.602 |
| r_chiral_restr | 0.083 |
| r_bond_refined_d | 0.013 |
| r_gen_planes_refined | 0.011 |
| r_gen_planes_other | 0.007 |
| 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 | 13913 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 680 |
| Heterogen Atoms | 266 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| REFMAC | refinement |
| DIALS | data reduction |
| DIALS | data scaling |
| REFMAC | phasing |