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Crystal Structure of the Lactate Dehydrogenase of Cyanobacterium Aponinum in its apo form.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 21 % Peg MME 550, 0.1 M NaCl, 0.1 M bicine pH 9
Crystal Properties Matthews coefficient Solvent content 3.6 65.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.797 α = 90 b = 103.797 β = 90 c = 197.824 γ = 90
Symmetry Space Group I 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2020-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9840 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.1 45.19 98.98 0.077 0.081 0.026 0.999 19.35 9.7 31611 40.99
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.176 94.4 0.913
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD FREE R-VALUE 2.1 37.96 1.35 31594 1580 99.01 0.185 0.183 0.1829 0.2234 0.2264 50.51
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 11.8209 f_angle_d 0.4519 f_chiral_restr 0.0437 f_plane_restr 0.0038 f_bond_d 0.0018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2478 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 37
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling CRANK2 phasing MxCuBE data collection Coot model building