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Crystal structure of D-Lactate dehydrogenase from aquifex aeolicus complexed with NAD and Lactic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DLD PDB ENTRY 2DLD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 25% PEG 200, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.64 53.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.938 α = 90 b = 94.432 β = 90 c = 188.849 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 225 mm CCD MIRRORS 2007-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 0.98 SRS PX10.1
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 2.12 38 95.2 0.088 12.2 8 88902 24.4
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 2.12 2.2 76.3 0.306 5.3 6.1 7005
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 PDB ENTRY 2DLD 2.12 38 88512 4439 95.31 0.167 0.164 0.1675 0.212 0.2106 RANDOM 29.453
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] -1.45 3.13 -1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.69 r_dihedral_angle_4_deg 15.89 r_dihedral_angle_3_deg 13.287 r_dihedral_angle_1_deg 5.963 r_scangle_it 3.749 r_scbond_it 2.347 r_angle_refined_deg 1.494 r_mcangle_it 1.429 r_angle_other_deg 0.895 r_mcbond_it 0.763
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.69 r_dihedral_angle_4_deg 15.89 r_dihedral_angle_3_deg 13.287 r_dihedral_angle_1_deg 5.963 r_scangle_it 3.749 r_scbond_it 2.347 r_angle_refined_deg 1.494 r_mcangle_it 1.429 r_angle_other_deg 0.895 r_mcbond_it 0.763 r_mcbond_other 0.198 r_chiral_restr 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10697 Nucleic Acid Atoms Solvent Atoms 853 Heterogen Atoms 452
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection