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Unspecific peroxygenase from Psathyrella aberdarensis (PabUPO-II) in complex with alpha-ionone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OXU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 1.85M ammonium sulphate, 100 mM BisTris pH 6.5
Soaking: 20 mM alpha-ionone 7 hours, cryoprotected with 20% glycerol
Crystal Properties Matthews coefficient Solvent content 4.29 71.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 270.969 α = 90 b = 75.05 β = 112.06 c = 106.056 γ = 90
Symmetry Space Group C 1 2 1
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 2021-06-19 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 2.2 49.19 98.5 0.116 0.13 0.056 0.995 10.5 5.2 508304
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 2.2 2.24 98 0.881 0.972 0.407 0.898 3.2 5.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2.2 49.19 93809 4833 98.21 0.18395 0.18246 0.21267 0.2288 RANDOM 43.29
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] -2.71 0.14 4.15 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.908 r_long_range_B_other 8.97 r_long_range_B_refined 8.948 r_scangle_other 7.521 r_dihedral_angle_2_deg 6.474 r_dihedral_angle_1_deg 6.427 r_mcangle_other 5.327 r_mcangle_it 5.326 r_scbond_it 4.969 r_scbond_other 4.938
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.908 r_long_range_B_other 8.97 r_long_range_B_refined 8.948 r_scangle_other 7.521 r_dihedral_angle_2_deg 6.474 r_dihedral_angle_1_deg 6.427 r_mcangle_other 5.327 r_mcangle_it 5.326 r_scbond_it 4.969 r_scbond_other 4.938 r_mcbond_it 3.635 r_mcbond_other 3.635 r_angle_refined_deg 1.525 r_angle_other_deg 0.565 r_chiral_restr 0.133 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 r_bond_other_d 0.002 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 8338 Nucleic Acid Atoms Solvent Atoms 562 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing