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Unspecific peroxygenase from Psathyrella aberdarensis (PabUPO-II)
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, HANGING DROP 291 2M ammonium sulphate, 100 mM HEPES pH 7.5
Cryoprotected with 20% glycerol
Crystal Properties Matthews coefficient Solvent content 4.27 71.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 272.859 α = 90 b = 74.84 β = 111.61 c = 105.579 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 2021-03-05 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) 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 2.3 49.08 99.8 0.077 0.088 0.041 12.6 4.5 88037
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 99.8 0.699 0.792 0.367 2.9 4.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2.3 48.43 83573 4443 99.68 0.195 0.19359 0.2006 0.22169 0.2255 RANDOM 46.727
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] -2.55 0.73 3.45 -1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.692 r_long_range_B_refined 7.136 r_long_range_B_other 7.135 r_dihedral_angle_1_deg 6.164 r_scangle_other 6.023 r_dihedral_angle_2_deg 5.128 r_scbond_it 4.401 r_mcangle_it 4.351 r_mcangle_other 4.351 r_scbond_other 4.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.692 r_long_range_B_refined 7.136 r_long_range_B_other 7.135 r_dihedral_angle_1_deg 6.164 r_scangle_other 6.023 r_dihedral_angle_2_deg 5.128 r_scbond_it 4.401 r_mcangle_it 4.351 r_mcangle_other 4.351 r_scbond_other 4.109 r_mcbond_it 3.052 r_mcbond_other 3.05 r_angle_refined_deg 1.349 r_angle_other_deg 0.484 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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 8470 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing