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Unspecific peroxygenase from Psathyrella aberdarensis, Grogu variant, in complex with alpha-ionone
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, 150mM Zn chloride
Cocrystallization 45mM alpha-ionone (incubation time: 30 minutes)
Crystal Properties Matthews coefficient Solvent content 3.06 59.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.587 α = 90 b = 76.587 β = 90 c = 271.901 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 2023-09-14 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 1.85 47.52 99.9 0.053 0.059 0.024 0.999 18 5.9 76832
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 1.85 1.89 99.4 0.473 0.518 0.211 0.899 3.1 6
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 1.85 47.52 72818 3895 99.86 0.16277 0.16129 0.1705 0.19126 0.1991 RANDOM 27.854
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] 0.42 0.21 0.42 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.409 r_dihedral_angle_1_deg 6.413 r_dihedral_angle_2_deg 6.181 r_long_range_B_refined 5.614 r_long_range_B_other 5.477 r_scangle_other 4.244 r_scbond_it 2.774 r_scbond_other 2.771 r_mcangle_it 2.698 r_mcangle_other 2.698
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.409 r_dihedral_angle_1_deg 6.413 r_dihedral_angle_2_deg 6.181 r_long_range_B_refined 5.614 r_long_range_B_other 5.477 r_scangle_other 4.244 r_scbond_it 2.774 r_scbond_other 2.771 r_mcangle_it 2.698 r_mcangle_other 2.698 r_mcbond_it 1.89 r_mcbond_other 1.889 r_angle_refined_deg 1.369 r_angle_other_deg 0.597 r_chiral_restr 0.07 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.006 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 772 Heterogen Atoms 403
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling REFMAC phasing