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Unspecific peroxygenase from Psathyrella aberdarensis, Grogu variant, in complex with anisole
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 6.5 291 10% (v/v) PEG 8000, 100mM MES pH 6.5, 200mM Zn acetate
Additive: 100mM magnesium chloride
Soaking 30mM anisole (time: 2h45)
Crystal Properties Matthews coefficient Solvent content 3.02 59.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.785 α = 90 b = 75.785 β = 90 c = 273.418 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 2023-04-21 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 2.5 47.39 99.9 0.077 0.084 0.032 0.998 14.3 6.8 30804
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 2.5 2.6 99.9 0.612 0.663 0.253 0.86 2.2 6.8
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 2.5 47.39 29148 1570 99.86 0.21674 0.21432 0.2168 0.26232 0.2626 RANDOM 54.755
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] -0.56 -0.28 -0.56 1.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.909 r_long_range_B_refined 9.802 r_long_range_B_other 9.779 r_dihedral_angle_1_deg 7.124 r_scangle_other 7.051 r_mcangle_it 6.81 r_mcangle_other 6.809 r_dihedral_angle_2_deg 6.308 r_scbond_it 4.65 r_scbond_other 4.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.909 r_long_range_B_refined 9.802 r_long_range_B_other 9.779 r_dihedral_angle_1_deg 7.124 r_scangle_other 7.051 r_mcangle_it 6.81 r_mcangle_other 6.809 r_dihedral_angle_2_deg 6.308 r_scbond_it 4.65 r_scbond_other 4.65 r_mcbond_other 4.518 r_mcbond_it 4.517 r_angle_refined_deg 1.364 r_angle_other_deg 0.482 r_chiral_restr 0.064 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_gen_planes_other 0.005 r_bond_other_d 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 5176 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 365
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling REFMAC phasing