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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 Other MODEL OF NATIVE D-LDH WHICH IS CURRENTLY BEING DEPOSITED IN THE PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 Orthorhombic crystals were grown by vapour diffusion from solutions of 20 % PEG
6K, 0.2 M ammonium sulphate in 0.1 M cacodylate buffer pH 6.5.
Crystal Properties Matthews coefficient Solvent content 2.91 57.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.3 α = 90 b = 188 β = 90 c = 193.4 γ = 90
Symmetry Space Group C 2 2 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 IMAGE PLATE MARRESEARCH MIRRORS 1998-12-01 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 1.9 19 98.4 0.047 16.1 3.1 132348 -3 0.215
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) 1.9 1.93 92.4 0.327 2.2
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 APART FROM THE LAST 3 CYCLES MODEL OF NATIVE D-LDH WHICH IS CURRENTLY BEING DEPOSITED IN THE PDB 1.9 19 132346 6647 98.4 0.204 0.204 0.201 0.259 RANDOM 0.327
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 36.1 p_staggered_tor 15 p_planar_tor 3.9 p_scangle_it 3.2 p_mcangle_it 2.5 p_scbond_it 2.5 p_mcbond_it 1.9 p_multtor_nbd 0.25 p_xhyhbond_nbd 0.197 p_xyhbond_nbd 0.197
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 36.1 p_staggered_tor 15 p_planar_tor 3.9 p_scangle_it 3.2 p_mcangle_it 2.5 p_scbond_it 2.5 p_mcbond_it 1.9 p_multtor_nbd 0.25 p_xhyhbond_nbd 0.197 p_xyhbond_nbd 0.197 p_singtor_nbd 0.19 p_chiral_restr 0.13 p_planar_d 0.035 p_angle_d 0.031 p_plane_restr 0.023 p_bond_d 0.013 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 10473 Nucleic Acid Atoms Solvent Atoms 900 Heterogen Atoms 55
Software Software Software Name Purpose AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling