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Crystal structure of human L-lactate Dehydrogenase B protein in complex with NADH, oxamate and sertraline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I0Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M ammonium formate, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.61 52.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.76 α = 90 b = 119.35 β = 90 c = 159.09 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS EIGER X 9M 2023-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98011 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.06 48.79 99.75 0.1352 0.988 12.18 13.4 100190 28.75
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.06 2.134 97.87 0.4555 0.691 1.77 13.3
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 2.06 48.79 1.34 100190 5007 99.26 0.1745 0.1724 0.1728 0.2156 0.2149 33.12
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 8.8341 f_angle_d 0.9669 f_chiral_restr 0.0582 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10425 Nucleic Acid Atoms Solvent Atoms 868 Heterogen Atoms 210
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing MxCuBE data collection Coot model building