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Dye-decolourising peroxidase DtpB (392 kGy)
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 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 2.59 52.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.965 α = 90 b = 121.963 β = 90 c = 199.6 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 undefined (fs) undefined (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 18590
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 2.4 40.15 100 0.9904 0.126 1.24 113.3 83736
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 2.4 2.46 0.46 0.927 0.39
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 2.4 40.15 79480 4178 99.93 0.24363 0.24207 0.2424 0.27311 0.2706 RANDOM 46.233
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 -0.04 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.962 r_dihedral_angle_2_deg 10.901 r_long_range_B_refined 10.779 r_long_range_B_other 10.779 r_scangle_other 8.588 r_dihedral_angle_1_deg 8.014 r_mcangle_it 7.724 r_mcangle_other 7.724 r_scbond_other 5.631 r_scbond_it 5.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.962 r_dihedral_angle_2_deg 10.901 r_long_range_B_refined 10.779 r_long_range_B_other 10.779 r_scangle_other 8.588 r_dihedral_angle_1_deg 8.014 r_mcangle_it 7.724 r_mcangle_other 7.724 r_scbond_other 5.631 r_scbond_it 5.63 r_mcbond_it 5.084 r_mcbond_other 5.084 r_angle_refined_deg 2.103 r_angle_other_deg 0.717 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 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 Non-Hydrogen Atoms Number Protein Atoms 13934 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 129
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling REFMAC phasing