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Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OXT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 291 1.6M sodium potassium phosphate pH 5.6, 3% MPD
Crystal Properties Matthews coefficient Solvent content 2.42 49.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.072 α = 90 b = 57.939 β = 109.36 c = 61.099 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 mirrors 2015-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9795 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 1.47 48.19 92.9 0.096 0.07 0.992 7.7 2.4 53236
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 1.47 1.5 93.4 0.65 0.52 0.624 2.5 2.2
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 MOLECULAR REPLACEMENT THROUGHOUT 5OXT 1.47 48.19 50634 2593 92.87 0.16446 0.16373 0.1737 0.17836 0.1883 RANDOM 11.654
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] -0.52 0.55 -0.83 0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.631 r_dihedral_angle_4_deg 13.866 r_dihedral_angle_3_deg 11.934 r_dihedral_angle_1_deg 5.691 r_long_range_B_refined 3.725 r_long_range_B_other 3.725 r_angle_refined_deg 1.298 r_scangle_other 1.021 r_angle_other_deg 0.948 r_mcangle_it 0.841
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.631 r_dihedral_angle_4_deg 13.866 r_dihedral_angle_3_deg 11.934 r_dihedral_angle_1_deg 5.691 r_long_range_B_refined 3.725 r_long_range_B_other 3.725 r_angle_refined_deg 1.298 r_scangle_other 1.021 r_angle_other_deg 0.948 r_mcangle_it 0.841 r_mcangle_other 0.84 r_scbond_it 0.602 r_scbond_other 0.602 r_mcbond_it 0.465 r_mcbond_other 0.464 r_chiral_restr 0.071 r_gen_planes_other 0.007 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 2514 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms 158
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing