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Unspecific peroxygenase from Marasmius rotula
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YOR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 295 20% PEG 3000, 0.1 M sodium acetate, pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.43 49.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.349 α = 90 b = 107.44 β = 90 c = 186.231 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 PIXEL DECTRIS PILATUS 6M 2020-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97924 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (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 1.45 73.44 99.4 0.094 0.037 12 6.1 175829
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.55 0.81 0.33 2.3
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 2YOR 1.45 73.44 167101 8668 99.3 0.1592 0.1579 0.1591 0.1842 0.1853 RANDOM 16.605
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] 0.93 0.05 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.356 r_dihedral_angle_4_deg 16.69 r_dihedral_angle_3_deg 12.57 r_dihedral_angle_1_deg 6.572 r_angle_refined_deg 1.835 r_angle_other_deg 1.56 r_chiral_restr 0.098 r_gen_planes_other 0.014 r_bond_refined_d 0.013 r_gen_planes_refined 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.356 r_dihedral_angle_4_deg 16.69 r_dihedral_angle_3_deg 12.57 r_dihedral_angle_1_deg 6.572 r_angle_refined_deg 1.835 r_angle_other_deg 1.56 r_chiral_restr 0.098 r_gen_planes_other 0.014 r_bond_refined_d 0.013 r_gen_planes_refined 0.013 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7274 Nucleic Acid Atoms Solvent Atoms 1058 Heterogen Atoms 211
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing