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The structure of D-mandelate dehydrogenase with L243W mutation
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 0.6 M NaCl, 0.05M Tris pH 8.5, 30% Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.43 49.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.54 α = 90 b = 130.91 β = 92.58 c = 58.09 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 2M 2023-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL17B 0.9786 NFPSS BL17B
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 45.97 94.9 0.997 16 6.7 40808
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 2.05 0.997
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2 45.97 38588 2117 94.58 0.21508 0.21313 0.25074 0.2612 RANDOM 27.588
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] 0.01 -0.74 -2.08 2.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.832 r_dihedral_angle_3_deg 13.263 r_dihedral_angle_1_deg 5.639 r_long_range_B_refined 4.598 r_long_range_B_other 4.558 r_dihedral_angle_4_deg 3.921 r_scangle_other 3.115 r_mcangle_it 2.496 r_mcangle_other 2.495 r_scbond_it 1.947
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.832 r_dihedral_angle_3_deg 13.263 r_dihedral_angle_1_deg 5.639 r_long_range_B_refined 4.598 r_long_range_B_other 4.558 r_dihedral_angle_4_deg 3.921 r_scangle_other 3.115 r_mcangle_it 2.496 r_mcangle_other 2.495 r_scbond_it 1.947 r_scbond_other 1.947 r_mcbond_it 1.603 r_mcbond_other 1.602 r_angle_refined_deg 1.311 r_angle_other_deg 0.782 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 4692 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing