Dye-decolourising peroxidase DtpB (448 kGy)
Serial Crystallography (SX)
Starting Model(s)
Initial Refinement Model(s) |
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Type | Source | Accession Code | Details |
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experimental model | PDB | 6YRJ | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | BATCH MODE | | 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 |
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Matthews coefficient | Solvent content |
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2.62 | 52.96 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 86.984 | α = 90 |
b = 121.963 | β = 90 |
c = 199.607 | γ = 90 |
Symmetry |
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Space Group | P 21 21 21 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | x-ray | 293 | PIXEL | DECTRIS PILATUS 6M | | 2019-09-19 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.9686 | Diamond | I24 |
Serial Crystallography
Sample delivery method |
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Diffraction ID | Description | Sample Delivery Method |
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1 | | fixed target |
Fixed Target |
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Diffraction ID | Description | Sample Holding | Support Base | Motion control | Details | Sample Solvent |
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1 | | silicone chip | | | | |
Measurement |
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Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
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1 | undefined (fs) | | | undefined (KeV) | |
Data Reduction |
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Diffraction ID | Frames Indexed | Crystal Hits | Frames Indexed | Latices Merged |
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1 | | 16846 | | |
Data Collection
Overall |
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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 |
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1 | 2.72 | 40.16 | 100 | 0.9925 | 0.115 | 1.2 | 140.5 | | 57840 | | | |
Highest Resolution Shell |
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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) |
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1 | 2.72 | 2.79 | | | 0.52 | 0.782 | 0.47 | | |
Refinement
Statistics |
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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 |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.72 | 40.16 | 54838 | 2931 | 99.93 | 0.23753 | 0.23496 | 0.2338 | 0.28625 | 0.2801 | RANDOM | 56.912 |
Temperature Factor Modeling |
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] |
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0.11 | | | -0.33 | | 0.22 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_3_deg | 16.676 |
r_long_range_B_refined | 14.687 |
r_long_range_B_other | 14.686 |
r_dihedral_angle_2_deg | 12.672 |
r_scangle_other | 12.453 |
r_mcangle_it | 11.552 |
r_mcangle_other | 11.551 |
r_dihedral_angle_1_deg | 8.995 |
r_scbond_it | 8.602 |
r_scbond_other | 8.602 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_3_deg | 16.676 |
r_long_range_B_refined | 14.687 |
r_long_range_B_other | 14.686 |
r_dihedral_angle_2_deg | 12.672 |
r_scangle_other | 12.453 |
r_mcangle_it | 11.552 |
r_mcangle_other | 11.551 |
r_dihedral_angle_1_deg | 8.995 |
r_scbond_it | 8.602 |
r_scbond_other | 8.602 |
r_mcbond_it | 7.97 |
r_mcbond_other | 7.97 |
r_angle_refined_deg | 2.692 |
r_angle_other_deg | 0.883 |
r_chiral_restr | 0.112 |
r_bond_refined_d | 0.014 |
r_gen_planes_refined | 0.01 |
r_gen_planes_other | 0.004 |
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 |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 13766 |
Nucleic Acid Atoms | |
Solvent Atoms | 2 |
Heterogen Atoms | 258 |
Software
Software |
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Software Name | Purpose |
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REFMAC | refinement |
DIALS | data reduction |
DIALS | data scaling |
REFMAC | phasing |