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Lactate Dehydrogenase in complex with hydroxylactam inhibitor compound 9: (6R)-3-[(2-chlorophenyl)sulfanyl]-4-hydroxy-6-(3-hydroxyphenyl)-6-(thiophen-3-yl)-5,6-dihydropyridin-2(1H)-one
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 7 292 PEG 3350, sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.15 42.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.624 α = 90 b = 81.229 β = 97.56 c = 104.797 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 110 PIXEL DECTRIS PILATUS 6M 2012-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.9795 SSRL BL11-1
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 2.05 37.8 98.2 0.058 16.6 3.5 -3 32.7
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 2.05 2.128 0.599 2.1 3.3
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1I10 2.05 37.8 74896 1571 98.01 0.17458 0.17359 0.1776 0.2207 0.2218 RANDOM 38.512
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] -0.54 -1.18 0.77 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.778 r_dihedral_angle_4_deg 17.973 r_dihedral_angle_3_deg 13.258 r_long_range_B_other 11.591 r_long_range_B_refined 11.537 r_scangle_other 10.746 r_scbond_it 8.338 r_scbond_other 8.3 r_mcangle_other 7.921 r_mcangle_it 7.916
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.778 r_dihedral_angle_4_deg 17.973 r_dihedral_angle_3_deg 13.258 r_long_range_B_other 11.591 r_long_range_B_refined 11.537 r_scangle_other 10.746 r_scbond_it 8.338 r_scbond_other 8.3 r_mcangle_other 7.921 r_mcangle_it 7.916 r_mcbond_it 6.374 r_mcbond_other 6.348 r_dihedral_angle_1_deg 5.432 r_angle_refined_deg 1.351 r_angle_other_deg 0.778 r_chiral_restr 0.145 r_gen_planes_refined 0.018 r_gen_planes_other 0.014 r_bond_refined_d 0.007 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10118 Nucleic Acid Atoms Solvent Atoms 569 Heterogen Atoms 353
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing