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The ternary structure of D-lactate dehydrogenase from Pseudomonas aeruginosa 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 298 1 mM NADH, 10 mM oxamate, 100 mM sodium formate, 10% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.59 65.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.69 α = 90 b = 155.69 β = 90 c = 230.011 γ = 120
Symmetry Space Group P 31 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 CCD ADSC QUANTUM 210 2013-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 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 2.2 37.4 98.8 0.129 0.045 0.997 13.8 8.3 161477
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 2.2 2.32 95.8 0.805 0.293 0.79 2.5 7.1
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 2.2 37.4 153341 8080 98.84 0.17206 0.17065 0.1792 0.19891 0.2033 RANDOM 32.734
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] 0.08 0.08 0.08 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.505 r_dihedral_angle_4_deg 22.622 r_dihedral_angle_3_deg 15.104 r_long_range_B_refined 7.348 r_long_range_B_other 7.348 r_scangle_other 5.773 r_dihedral_angle_1_deg 5.709 r_scbond_it 3.847 r_scbond_other 3.847 r_mcangle_it 3.183
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.505 r_dihedral_angle_4_deg 22.622 r_dihedral_angle_3_deg 15.104 r_long_range_B_refined 7.348 r_long_range_B_other 7.348 r_scangle_other 5.773 r_dihedral_angle_1_deg 5.709 r_scbond_it 3.847 r_scbond_other 3.847 r_mcangle_it 3.183 r_mcangle_other 3.183 r_mcbond_it 2.295 r_mcbond_other 2.295 r_angle_refined_deg 1.857 r_angle_other_deg 1.589 r_chiral_restr 0.112 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_bond_other_d 0.011 r_gen_planes_other 0.009 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 15290 Nucleic Acid Atoms Solvent Atoms 908 Heterogen Atoms 366
Software Software Software Name Purpose REFMAC refinement ADSC data collection SCALA data scaling BUCCANEER model building