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Unspecific Peroxygenase from Daldinia childiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 20% (w/v) PEG 6000; 0.2 M CaCl2 dihydrate; 0.1 M MES pH 6.0
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.604 α = 90 b = 78.049 β = 95.18 c = 62.585 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 120 PIXEL DECTRIS EIGER2 XE 16M 2024-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976250 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.88 40.67 99.7 0.14 0.08 1 7.4 7 31736 21
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.92 1.18 0.72 0.69 1.5
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 1.88 40.67 30097 1612 99.56 0.20743 0.20461 0.2121 0.26234 0.2672 RANDOM 33.275
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] -3.15 1.37 -2.92 5.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.582 r_dihedral_angle_2_deg 8.89 r_long_range_B_refined 6.945 r_long_range_B_other 6.836 r_dihedral_angle_1_deg 6.146 r_scangle_other 5.133 r_mcangle_it 4.422 r_mcangle_other 4.421 r_scbond_other 3.553 r_scbond_it 3.552
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.582 r_dihedral_angle_2_deg 8.89 r_long_range_B_refined 6.945 r_long_range_B_other 6.836 r_dihedral_angle_1_deg 6.146 r_scangle_other 5.133 r_mcangle_it 4.422 r_mcangle_other 4.421 r_scbond_other 3.553 r_scbond_it 3.552 r_mcbond_it 3.152 r_mcbond_other 3.152 r_angle_refined_deg 1.644 r_angle_other_deg 0.594 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 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 3294 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing