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INSIGHTS INTO DOMAIN CLOSURE, SUBSTRATE SPECIFICITY AND CATALYSIS OF D-LACTATE DEHYDROGENASE FROM LACTOBACILLUS BULGARICUS
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 5 pH 5.0
Crystal Properties Matthews coefficient Solvent content 2.45 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.4 α = 90 b = 79.4 β = 90 c = 228.5 γ = 90
Symmetry Space Group P 43 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 298 IMAGE PLATE MARRESEARCH MIRRORS 1994-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 2.2 15 98.7 0.071 19.4 5.8 38147 2 36.1
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) 2.2 2.24 93.3 0.21 3.73 6.82
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT (EXCEPT FOR THE LAST 2 REFINEMENT CYCLES) PDB ENTRY 2DLD 2.2 15 37544 1884 98.7 0.209 0.207 0.1974 0.271 RANDOM 44.4
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 p_transverse_tor 35.6 p_staggered_tor 18.8 p_planar_tor 4.3 p_mcangle_it 1.5 p_scangle_it 1.4 p_mcbond_it 0.8 p_scbond_it 0.8 p_multtor_nbd 0.3 p_xhyhbond_nbd 0.23 p_xyhbond_nbd 0.23
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 35.6 p_staggered_tor 18.8 p_planar_tor 4.3 p_mcangle_it 1.5 p_scangle_it 1.4 p_mcbond_it 0.8 p_scbond_it 0.8 p_multtor_nbd 0.3 p_xhyhbond_nbd 0.23 p_xyhbond_nbd 0.23 p_singtor_nbd 0.2 p_planar_d 0.033 p_chiral_restr 0.03 p_plane_restr 0.026 p_angle_d 0.025 p_bond_d 0.015 p_angle_deg p_hb_or_metal_coord p_orthonormal_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5207 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 93
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement