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Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita, in complex with naphthalene
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 1.4M sodium potassium phosphate pH 5.6, 3% MPD, soaking 20mM naphthalene, 20% methanol
Crystal Properties Matthews coefficient Solvent content 2.42 49.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.187 α = 90 b = 57.743 β = 109.46 c = 61.104 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) Rrim 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 1.43 48.26 98.5 0.089 0.043 0.997 10.8 4.9 61029
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 1.43 1.45 91 0.651 0.349 0.752 2 4.1
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 1.43 48.26 57996 3013 98.24 0.15659 0.15538 0.1623 0.18024 0.1872 RANDOM 14.306
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] -0.37 0.39 -0.96 0.84
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 39.666 r_dihedral_angle_2_deg 33.423 r_dihedral_angle_4_deg 17.276 r_dihedral_angle_3_deg 11.861 r_dihedral_angle_1_deg 5.684 r_sphericity_bonded 4.497 r_long_range_B_refined 4.399 r_long_range_B_other 4.123 r_scangle_other 1.408 r_angle_refined_deg 1.405
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 39.666 r_dihedral_angle_2_deg 33.423 r_dihedral_angle_4_deg 17.276 r_dihedral_angle_3_deg 11.861 r_dihedral_angle_1_deg 5.684 r_sphericity_bonded 4.497 r_long_range_B_refined 4.399 r_long_range_B_other 4.123 r_scangle_other 1.408 r_angle_refined_deg 1.405 r_angle_other_deg 1.243 r_mcangle_it 0.976 r_mcangle_other 0.976 r_scbond_it 0.854 r_scbond_other 0.853 r_mcbond_it 0.592 r_mcbond_other 0.575 r_chiral_restr 0.084 r_gen_planes_other 0.011 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2514 Nucleic Acid Atoms Solvent Atoms 447 Heterogen Atoms 202
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing