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SFX structure of dye-type peroxidase DtpB D152A/N245A variant in the ferric state
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 buffer, 150mM NaCl pH 7 mixed with 125 mM mM MgCl2, 125 mM HEPES pH 7.5, 18% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.58 52.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.95 α = 90 b = 121.83 β = 90 c = 199.5 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 301 CCD MPCCD 2021-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL2 1.127 SACLA BL2
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 2.2 32.1 100 0.926 0.219 3.88 1040 108174
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 2.2 2.24 0.509 1.088
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6YRJ 2.2 32.1 102375 5434 99.67 0.2206 0.2181 0.2688 0.2796 RANDOM 32.316
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] 0.4 -1.4 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.715 r_dihedral_angle_4_deg 18.142 r_dihedral_angle_3_deg 15.214 r_dihedral_angle_1_deg 7.122 r_angle_refined_deg 1.898 r_angle_other_deg 1.388 r_chiral_restr 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_gen_planes_other 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.715 r_dihedral_angle_4_deg 18.142 r_dihedral_angle_3_deg 15.214 r_dihedral_angle_1_deg 7.122 r_angle_refined_deg 1.898 r_angle_other_deg 1.388 r_chiral_restr 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13889 Nucleic Acid Atoms Solvent Atoms 687 Heterogen Atoms 259
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling REFMAC phasing