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Mandelate oxidase mutant-Y128F with 4-hydroxymandelic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SGZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 35% Tascimate, 0.1M Bis-Tris propane pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.5 64.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.836 α = 90 b = 137.836 β = 90 c = 111.469 γ = 90
Symmetry Space Group I 4 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300HE 2017-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.35 30 100 0.051 0.02 36.09 12.2 116144
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 1.35 1.4 100 0.746 0.269 0.844 2.69 12
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 3SGZ 1.35 30 106077 5435 95.92 0.16742 0.1668 0.1765 0.1796 0.1872 RANDOM 17.726
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] -0.05 -0.05 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.944 r_dihedral_angle_4_deg 14.252 r_dihedral_angle_3_deg 12.101 r_long_range_B_refined 5.973 r_dihedral_angle_1_deg 5.67 r_long_range_B_other 5.457 r_scangle_other 2.127 r_mcangle_it 1.637 r_mcangle_other 1.637 r_angle_refined_deg 1.381
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.944 r_dihedral_angle_4_deg 14.252 r_dihedral_angle_3_deg 12.101 r_long_range_B_refined 5.973 r_dihedral_angle_1_deg 5.67 r_long_range_B_other 5.457 r_scangle_other 2.127 r_mcangle_it 1.637 r_mcangle_other 1.637 r_angle_refined_deg 1.381 r_scbond_it 1.311 r_scbond_other 1.31 r_mcbond_it 0.954 r_mcbond_other 0.951 r_angle_other_deg 0.924 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 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 2498 Nucleic Acid Atoms Solvent Atoms 401 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing