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Dye-decolourising peroxidase DtpB (56 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 20mM NaPi, 150mM 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 = 86.729 α = 90 b = 121.782 β = 90 c = 199.52 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 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 10 (fs) undefined (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 23518
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 1.75 40.05 100 0.975 0.142 2 64.3 212573
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 1.75 1.78 0.5 0.794
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.75 40.05 201787 10674 99.97 0.19856 0.19743 0.21972 0.2127 RANDOM 28.44
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] 0.18 -0.56 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.059 r_dihedral_angle_2_deg 12.226 r_long_range_B_other 7.668 r_long_range_B_refined 7.664 r_dihedral_angle_1_deg 6.757 r_scangle_other 6.557 r_scbond_it 4.287 r_scbond_other 4.287 r_mcangle_it 4.202 r_mcangle_other 4.201
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.059 r_dihedral_angle_2_deg 12.226 r_long_range_B_other 7.668 r_long_range_B_refined 7.664 r_dihedral_angle_1_deg 6.757 r_scangle_other 6.557 r_scbond_it 4.287 r_scbond_other 4.287 r_mcangle_it 4.202 r_mcangle_other 4.201 r_mcbond_it 2.746 r_mcbond_other 2.746 r_angle_refined_deg 1.931 r_angle_other_deg 0.656 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 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 14178 Nucleic Acid Atoms Solvent Atoms 457 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling REFMAC phasing