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The structure of D-mandelate dehydrogenase with L103G and T143G mutations
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WFI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289.15 0.4 M NaCl, 0.05M Tris pH 8.5, 25% Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.4 48.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.62 α = 90 b = 131.99 β = 90 c = 58.64 γ = 90
Symmetry Space Group C 1 2 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 PILATUS3 6M 2023-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL18U 0.9786 NFPSS BL18U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.55 44.96 96.8 0.996 9.7 2.5 19800
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.66 0.996
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.55 44.96 18936 863 96.6 0.24834 0.24622 0.2444 0.29449 0.2848 RANDOM 42.329
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] -10.25 -1.58 -1.05 11.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.622 r_dihedral_angle_3_deg 14.698 r_dihedral_angle_4_deg 11.167 r_dihedral_angle_1_deg 5.539 r_long_range_B_refined 2.763 r_long_range_B_other 2.753 r_mcangle_it 1.284 r_mcangle_other 1.284 r_angle_refined_deg 1.132 r_angle_other_deg 0.745
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.622 r_dihedral_angle_3_deg 14.698 r_dihedral_angle_4_deg 11.167 r_dihedral_angle_1_deg 5.539 r_long_range_B_refined 2.763 r_long_range_B_other 2.753 r_mcangle_it 1.284 r_mcangle_other 1.284 r_angle_refined_deg 1.132 r_angle_other_deg 0.745 r_scangle_other 0.699 r_mcbond_it 0.694 r_mcbond_other 0.694 r_scbond_it 0.334 r_scbond_other 0.334 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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 4678 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction HKL-3000 data scaling HKL-3000 phasing