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The crystal structure of Mandelate oxidase with (S)-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 3.46 64.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.829 α = 90 b = 137.829 β = 90 c = 111.28 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 2017-07-28 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) 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 1.32 30 100 0.038 43.5 12.2 124343
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.32 1.37 100 0.8 2.5 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 1.32 30 112040 5897 94.78 0.17568 0.17505 0.1831 0.18797 0.1873 RANDOM 19.763
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] -0.03 -0.03 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.736 r_dihedral_angle_4_deg 17.098 r_dihedral_angle_3_deg 13.222 r_dihedral_angle_1_deg 5.976 r_long_range_B_refined 5.618 r_long_range_B_other 5.195 r_scangle_other 2.683 r_mcangle_it 2.125 r_mcangle_other 2.124 r_scbond_it 1.635
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.736 r_dihedral_angle_4_deg 17.098 r_dihedral_angle_3_deg 13.222 r_dihedral_angle_1_deg 5.976 r_long_range_B_refined 5.618 r_long_range_B_other 5.195 r_scangle_other 2.683 r_mcangle_it 2.125 r_mcangle_other 2.124 r_scbond_it 1.635 r_scbond_other 1.635 r_angle_refined_deg 1.416 r_mcbond_it 1.266 r_mcbond_other 1.263 r_angle_other_deg 0.785 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2644 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing