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Dye-decolourising peroxidase DtpB XRPP experiment (500 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 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 2.64 53.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.07 α = 90 b = 122.745 β = 90 c = 199.978 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 MX300-HS 2022-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL2 1.1263 SACLA BL2
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 10 (fs) 30 11 (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 6831
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 1.9 34.97 100 0.986 0.268 6.4 57.3 168768
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 1.9 1.949 0.35 1.395 1.1 56.8
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 1.9 34.97 160251 8457 99.89 0.22641 0.22398 0.2282 0.27242 0.2741 RANDOM 25.696
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] -0.2 0.6 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.914 r_dihedral_angle_2_deg 10.857 r_dihedral_angle_1_deg 7.114 r_long_range_B_refined 6.971 r_long_range_B_other 6.969 r_scangle_other 5.457 r_mcangle_it 4.445 r_mcangle_other 4.445 r_scbond_it 3.662 r_scbond_other 3.662
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.914 r_dihedral_angle_2_deg 10.857 r_dihedral_angle_1_deg 7.114 r_long_range_B_refined 6.971 r_long_range_B_other 6.969 r_scangle_other 5.457 r_mcangle_it 4.445 r_mcangle_other 4.445 r_scbond_it 3.662 r_scbond_other 3.662 r_mcbond_it 3.177 r_mcbond_other 3.175 r_angle_refined_deg 2.216 r_angle_other_deg 0.761 r_chiral_restr 0.109 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 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 13923 Nucleic Acid Atoms Solvent Atoms 705 Heterogen Atoms 263
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling REFMAC phasing