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The ternary structure of D-lactate dehydrogenase from Fusobacterium nucleatum with NADH and oxamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J49
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 2 mM NADH, 25 mM oxamate, 100 mM acetate buffer pH 5, 4% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.58 52.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.23 α = 90 b = 159.74 β = 90 c = 90 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 210 2013-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 0.97911 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.3 42.01 100 0.125 0.05 0.996 13.5 7.2 75787
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.42 100 0.64 0.254 0.738 3.2 7.3
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 1J49 2.3 42.01 71921 3810 99.97 0.22679 0.22546 0.2283 0.25142 0.2506 RANDOM 33.925
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 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.99 r_dihedral_angle_4_deg 24.522 r_dihedral_angle_3_deg 16.069 r_dihedral_angle_1_deg 6.21 r_long_range_B_refined 3.963 r_long_range_B_other 3.96 r_scangle_other 2.668 r_mcangle_it 2.405 r_mcangle_other 2.405 r_scbond_it 1.638
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.99 r_dihedral_angle_4_deg 24.522 r_dihedral_angle_3_deg 16.069 r_dihedral_angle_1_deg 6.21 r_long_range_B_refined 3.963 r_long_range_B_other 3.96 r_scangle_other 2.668 r_mcangle_it 2.405 r_mcangle_other 2.405 r_scbond_it 1.638 r_scbond_other 1.638 r_angle_refined_deg 1.629 r_mcbond_it 1.541 r_mcbond_other 1.541 r_angle_other_deg 1.332 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.008 r_gen_planes_other 0.007 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 10490 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 200
Software Software Software Name Purpose REFMAC refinement ADSC data collection SCALA data scaling BUCCANEER model building