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Mutational and structural analysis of an ancestral D-type dye decolorizing peroxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FSK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 294 2 M Ammonium sulfate, 0.1 M MES
Crystal Properties Matthews coefficient Solvent content 2.1 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.085 α = 90 b = 69.107 β = 90 c = 114.39 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 100 PIXEL DECTRIS EIGER2 XE 16M 2020-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.65 59.15 97 0.065 0.068 0.02 0.999 18.2 10.3 55396
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 75.2 0.759 0.874 0.422 0.682 3.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6FSK 1.65 59.15 52613 2715 96.91 0.1625 0.1608 0.1733 0.1961 0.2021 RANDOM 27.675
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] 1.31 -0.89 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.858 r_dihedral_angle_4_deg 21.812 r_dihedral_angle_3_deg 12.173 r_dihedral_angle_1_deg 7.108 r_angle_refined_deg 1.686 r_angle_other_deg 1.431 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.858 r_dihedral_angle_4_deg 21.812 r_dihedral_angle_3_deg 12.173 r_dihedral_angle_1_deg 7.108 r_angle_refined_deg 1.686 r_angle_other_deg 1.431 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3616 Nucleic Acid Atoms Solvent Atoms 398 Heterogen Atoms 86
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction PHASER phasing