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The ternary structure of D-mandelate dehydrogenase with NADH and anilino(oxo)acetate
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 5 278 0.1 M cacodylate-Na (pH 5.0), 0.17 M ammonium sulfate, 22.5% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.83 56.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.3 α = 90 b = 111.95 β = 96.65 c = 108.94 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 CCD ADSC QUANTUM 210 2014-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 43.98 99.6 8.7 3.6 89403
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 98.7 2.5 3.5
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 3WFI 2.4 29.82 84874 4479 99.54 0.18588 0.18413 0.1935 0.21831 0.2244 RANDOM 37.36
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.537 r_dihedral_angle_4_deg 20.834 r_dihedral_angle_3_deg 17.198 r_long_range_B_refined 6.498 r_long_range_B_other 6.487 r_dihedral_angle_1_deg 5.847 r_scangle_other 4.88 r_mcangle_it 3.575 r_mcangle_other 3.575 r_scbond_it 3.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.537 r_dihedral_angle_4_deg 20.834 r_dihedral_angle_3_deg 17.198 r_long_range_B_refined 6.498 r_long_range_B_other 6.487 r_dihedral_angle_1_deg 5.847 r_scangle_other 4.88 r_mcangle_it 3.575 r_mcangle_other 3.575 r_scbond_it 3.136 r_scbond_other 3.136 r_mcbond_it 2.321 r_mcbond_other 2.321 r_angle_refined_deg 1.759 r_angle_other_deg 1.521 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.009 r_gen_planes_other 0.008 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 12866 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 478
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOLREP phasing