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Structural Characterisation of the Apo-form of Human Lactate Dehydrogenase M Isozyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I10
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 10% PEG 8000, 100 mM HEPES pH 7.5, 20 % ethylene glycol, 10 % Acetonitrile, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.28 62.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.652 α = 90 b = 84.652 β = 90 c = 275.969 γ = 90
Symmetry Space Group P 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 neutron 77 PIXEL DECTRIS PILATUS 2M M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9173 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.1 29.755 94.6 0.077 14.9 6.6 56283 56283 30.17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 74.8 0.482 0.482 1.5 5.7
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 1i10 2.1 29.755 1.34 56269 2847 94.26 0.1648 0.1639 0.1655 0.1816 0.184 36.4352
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 f_dihedral_angle_d 12.959 f_angle_d 1.09 f_chiral_restr 0.071 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5134 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHASER phasing BUSTER-TNT refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling