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Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita, in complex with 1-naphthol (I)
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 1.6M sodium potassium phosphate pH 5.6, 3% MPD, soaking 100mM 1-Naphthol, 20% methanol
Crystal Properties Matthews coefficient Solvent content 2.42 49.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.086 α = 90 b = 57.799 β = 109.89 c = 60.691 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 2015-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9792 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 1.13 48.04 99 0.066 0.028 0.999 13.1 5.9 124527
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.13 1.14 0.605 0.369 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 FOURIER SYNTHESIS THROUGHOUT 5OXU 1.13 48.04 118360 6134 98.97 0.16642 0.16596 0.1851 0.17536 0.1948 RANDOM 12.996
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] -0.27 0.45 -0.68 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.44 r_rigid_bond_restr 26.588 r_dihedral_angle_4_deg 17.054 r_dihedral_angle_3_deg 11.918 r_dihedral_angle_1_deg 5.824 r_long_range_B_refined 3.985 r_long_range_B_other 3.985 r_sphericity_bonded 3.343 r_angle_refined_deg 1.351 r_scangle_other 1.175
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.44 r_rigid_bond_restr 26.588 r_dihedral_angle_4_deg 17.054 r_dihedral_angle_3_deg 11.918 r_dihedral_angle_1_deg 5.824 r_long_range_B_refined 3.985 r_long_range_B_other 3.985 r_sphericity_bonded 3.343 r_angle_refined_deg 1.351 r_scangle_other 1.175 r_angle_other_deg 0.961 r_mcangle_it 0.925 r_mcangle_other 0.924 r_scbond_it 0.723 r_scbond_other 0.723 r_mcbond_other 0.516 r_mcbond_it 0.515 r_chiral_restr 0.082 r_gen_planes_other 0.009 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.004 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_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2510 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms 206
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing