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Unspecific peroxygenase from Psathyrella aberdarensis, Grogu variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9HE6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 10% (v/v) PEG 8000, 100mM MES pH 6.5, 200mM Zn acetate
Crystal Properties Matthews coefficient Solvent content 3.09 60.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.677 α = 90 b = 76.677 β = 90 c = 273.793 γ = 120
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 PILATUS 6M KB MIRRORS 2022-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979 ALBA XALOC
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 2.55 47.71 100 0.107 0.119 0.052 0.996 10.6 5.1 29600
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 2.55 2.66 99.9 0.613 0.683 0.299 0.876 3.9 5.1
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 2.55 47.71 28052 1441 99.82 0.19369 0.19094 0.1936 0.24731 0.246 RANDOM 53.607
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] 0.89 0.44 0.89 -2.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.515 r_long_range_B_refined 10.064 r_long_range_B_other 10.052 r_scangle_other 8.32 r_dihedral_angle_2_deg 7.427 r_dihedral_angle_1_deg 6.742 r_mcangle_it 6.455 r_mcangle_other 6.455 r_scbond_it 5.855 r_scbond_other 5.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.515 r_long_range_B_refined 10.064 r_long_range_B_other 10.052 r_scangle_other 8.32 r_dihedral_angle_2_deg 7.427 r_dihedral_angle_1_deg 6.742 r_mcangle_it 6.455 r_mcangle_other 6.455 r_scbond_it 5.855 r_scbond_other 5.8 r_mcbond_it 4.694 r_mcbond_other 4.693 r_angle_refined_deg 1.532 r_angle_other_deg 0.601 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 0.005 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 5615 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling REFMAC phasing