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Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita, in complex with veratryl alcohol
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 5.6 291 1.6 M sodium potassium phosphate pH 5.6, soaking 50mM veratryl alcohol
Crystal Properties Matthews coefficient Solvent content 2.42 49.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.074 α = 90 b = 57.982 β = 109.85 c = 60.923 γ = 90
Symmetry Space Group P 1 21 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 mirror 2014-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9793 ALBA XALOC
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 1.53 48.04 99.2 0.091 0.042 0.997 11.7 5.4 50107
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 1.53 1.56 97.7 0.608 0.277 0.869 3.1 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5OXU 1.53 48.04 47583 2502 98.99 0.15435 0.15369 0.1584 0.16745 0.1729 RANDOM 16.315
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] -0.51 0.89 -1.23 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.41 r_dihedral_angle_4_deg 16.327 r_dihedral_angle_3_deg 11.795 r_dihedral_angle_1_deg 5.574 r_long_range_B_refined 3.572 r_long_range_B_other 3.571 r_scangle_other 1.378 r_angle_refined_deg 1.288 r_mcangle_it 1.073 r_mcangle_other 1.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.41 r_dihedral_angle_4_deg 16.327 r_dihedral_angle_3_deg 11.795 r_dihedral_angle_1_deg 5.574 r_long_range_B_refined 3.572 r_long_range_B_other 3.571 r_scangle_other 1.378 r_angle_refined_deg 1.288 r_mcangle_it 1.073 r_mcangle_other 1.073 r_angle_other_deg 0.969 r_scbond_it 0.833 r_scbond_other 0.833 r_mcbond_it 0.61 r_mcbond_other 0.609 r_chiral_restr 0.071 r_bond_refined_d 0.006 r_gen_planes_other 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.003 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 2521 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 162
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing