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Structure of Salmonella D-Lactate Dehydrogenase in complex with NADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other APO STRUCTURE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.1 M [ IMIDAZOLE; MES (ACID) ] PH 6.5; 0.06M [ MGCL2; CACL2 ]; 30% [ GLYCEROL; PEG 4K ]
Crystal Properties Matthews coefficient Solvent content 2.47 50.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.35 α = 90 b = 60.7 β = 106.92 c = 130.39 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 MARRESEARCH 2010-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.18 51.22 96.1 0.07 11.5 2.9 86835 3.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.18 2.3 97.3 0.29 3.8 2.9
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 APO STRUCTURE 2.18 105.57 79013 4173 95.8 0.17918 0.17679 0.1964 0.22396 0.2332 RANDOM 29.889
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 37.69 r_dihedral_angle_4_deg 16.645 r_dihedral_angle_3_deg 14.905 r_dihedral_angle_1_deg 6.709 r_mcangle_it 4.019 r_scbond_it 3.357 r_mcbond_it 2.572 r_mcbond_other 2.572 r_angle_refined_deg 1.848 r_angle_other_deg 0.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.69 r_dihedral_angle_4_deg 16.645 r_dihedral_angle_3_deg 14.905 r_dihedral_angle_1_deg 6.709 r_mcangle_it 4.019 r_scbond_it 3.357 r_mcbond_it 2.572 r_mcbond_other 2.572 r_angle_refined_deg 1.848 r_angle_other_deg 0.892 r_chiral_restr 0.108 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 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_mcangle_other 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 10360 Nucleic Acid Atoms Solvent Atoms 483 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing