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Dye-decolourising peroxidase DtpB (280 kGy)
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 2.61 52.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.891 α = 90 b = 121.924 β = 90 c = 199.572 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 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 21216
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 2.02 40.12 100 0.9876 0.126 1.6 85.2 139296
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 2.02 2.07 0.57 0.567 0.5
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 2.02 40.12 132270 6929 99.95 0.23019 0.22874 0.2318 0.25782 0.2571 RANDOM 35.109
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.527 r_dihedral_angle_2_deg 12.958 r_long_range_B_other 8.874 r_long_range_B_refined 8.873 r_dihedral_angle_1_deg 7.616 r_scangle_other 7.401 r_mcangle_it 5.77 r_mcangle_other 5.769 r_scbond_it 4.908 r_scbond_other 4.908
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.527 r_dihedral_angle_2_deg 12.958 r_long_range_B_other 8.874 r_long_range_B_refined 8.873 r_dihedral_angle_1_deg 7.616 r_scangle_other 7.401 r_mcangle_it 5.77 r_mcangle_other 5.769 r_scbond_it 4.908 r_scbond_other 4.908 r_mcbond_it 3.814 r_mcbond_other 3.812 r_angle_refined_deg 2.16 r_angle_other_deg 0.727 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.005 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 13801 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 272
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling REFMAC phasing