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The complex structure of D-mandelate dehydrogenase with NADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WFI PDB ENTRY 3WFI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 0.1M Tris-HCl (pH 7.0), 0.2M calcium acetate, 20% PEG 3350, 10mM NADH, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.6 52.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.65 α = 90 b = 103.44 β = 90.01 c = 119.74 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 2012-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.00 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 2.8 20 98 69522 68132
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 2.8 2.87 98
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 3WFI 2.8 19.97 66195 64680 3439 97.71 0.24215 0.24215 0.23876 0.30582 0.2979 RANDOM 45.94
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] 2.13 0.77 -3.26 1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.428 r_dihedral_angle_4_deg 20.784 r_dihedral_angle_3_deg 20.339 r_dihedral_angle_1_deg 7.701 r_angle_refined_deg 2.278 r_angle_other_deg 1.773 r_chiral_restr 0.12 r_bond_refined_d 0.021 r_gen_planes_refined 0.014 r_bond_other_d 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.428 r_dihedral_angle_4_deg 20.784 r_dihedral_angle_3_deg 20.339 r_dihedral_angle_1_deg 7.701 r_angle_refined_deg 2.278 r_angle_other_deg 1.773 r_chiral_restr 0.12 r_bond_refined_d 0.021 r_gen_planes_refined 0.014 r_bond_other_d 0.013 r_gen_planes_other 0.011 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17616 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 352
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling