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Dye-decolourising peroxidase DtpB XRPP experiment (1000 kGy)-PUMP
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 7.5 291 6.2 mg/mL of protein in 20mM Sodium phosphate, 150mM NaCl pH 7 was mixed with 125 mM MgCl2, 125 mM HEPES, 20% PEG 4000 pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.64 53.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.054 α = 90 b = 122.576 β = 90 c = 200.237 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 1.1264 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 11890
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 46.05 100 0.914 0.217 5.9 94.8 168749
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 0.25 1.612
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 41.05 160314 8458 99.97 0.21737 0.21506 0.2189 0.26108 0.2624 RANDOM 29.837
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] 0.04 0.22 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.278 r_dihedral_angle_2_deg 11.913 r_long_range_B_refined 7.563 r_long_range_B_other 7.56 r_dihedral_angle_1_deg 7.094 r_scangle_other 6.126 r_mcangle_it 4.643 r_mcangle_other 4.643 r_scbond_it 4.089 r_scbond_other 4.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.278 r_dihedral_angle_2_deg 11.913 r_long_range_B_refined 7.563 r_long_range_B_other 7.56 r_dihedral_angle_1_deg 7.094 r_scangle_other 6.126 r_mcangle_it 4.643 r_mcangle_other 4.643 r_scbond_it 4.089 r_scbond_other 4.088 r_mcbond_it 3.35 r_mcbond_other 3.349 r_angle_refined_deg 2.048 r_angle_other_deg 0.695 r_chiral_restr 0.1 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 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 648 Heterogen Atoms 265
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling REFMAC phasing