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Crystal structure of Lactate dehydrogenase in complex with 4-((4-(1-methyl-1H-imidazole-2-carbonyl)phenyl)amino)-4-oxo-2-(4-(trifluoromethyl)phenyl)butanoic acid (S-enantiomer, monoclinic P form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5W8J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 Index HT C9: 1.1 M sodium malonate, 0.1 M HEPES pH 7.0, 0.5 %v/v Jeffamine ED-2001, LDHA at 11.9 mg/mL. 2mM inhibitor added prior to crystallization. plate Anne-clover-6, A2. Puck: PSL-1914, Cryo: 3.4 M sodium malonate pH 7.5.
Crystal Properties Matthews coefficient Solvent content 1.92 36.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.282 α = 90 b = 99.24 β = 98.69 c = 82.657 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER2 XE 9M 2023-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9795 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.85 49.62 100 0.122 0.133 0.052 0.997 9.4 6.4 100987
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 99.9 1.329 1.442 0.554 0.629 6.7
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 MOLECULAR REPLACEMENT FREE R-VALUE 1.85 40.85 1.01 100926 5021 99.93 0.156 0.1541 0.1637 0.1917 0.1967
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 12.986 f_angle_d 0.761 f_chiral_restr 0.052 f_plane_restr 0.008 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10012 Nucleic Acid Atoms Solvent Atoms 560 Heterogen Atoms 118
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing