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Unspecific peroxygenase from Psathyrella aberdarensis (PabUPO-II) in complex with 2,6-dimethoxyphenol
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, 0.1M HEPES pH 7.5, additive: 30% v/v ethylene glycol
Soaking: 25 mM 2,6-dimethoxyphenol 2h30, cryoprotected with 20% glycerol
Crystal Properties Matthews coefficient Solvent content 4.28 71.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 271.298 α = 90 b = 74.502 β = 111.8 c = 106.15 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 2024-02-01 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 1.9 48.53 99.8 0.059 0.064 0.024 0.999 17.8 6.8 154714
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 1.9 1.93 99.8 1.172 1.271 0.486 0.839 1.7 6.7
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 1.9 45.93 146839 7875 99.83 0.20071 0.19972 0.21885 0.221 RANDOM 44.174
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] -3 0.51 3.68 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.115 r_dihedral_angle_2_deg 10.839 r_long_range_B_other 7.509 r_long_range_B_refined 7.492 r_dihedral_angle_1_deg 6.232 r_scangle_other 5.973 r_mcangle_it 4.359 r_mcangle_other 4.358 r_scbond_it 4.022 r_scbond_other 4.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.115 r_dihedral_angle_2_deg 10.839 r_long_range_B_other 7.509 r_long_range_B_refined 7.492 r_dihedral_angle_1_deg 6.232 r_scangle_other 5.973 r_mcangle_it 4.359 r_mcangle_other 4.358 r_scbond_it 4.022 r_scbond_other 4.017 r_mcbond_it 3.193 r_mcbond_other 3.193 r_angle_refined_deg 1.413 r_angle_other_deg 0.534 r_chiral_restr 0.13 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 0.003 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 8398 Nucleic Acid Atoms Solvent Atoms 705 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing