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Lactate dehydrogenase A in complex with a trisubstituted piperidine-2,4-dione inhibitor GNE-140
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 7 293 PEG3350, malonate pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.23 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.164 α = 90 b = 81.288 β = 98.31 c = 102.47 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 CCD ADSC QUANTUM 315r 2013-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9793 SSRF BL17U
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 2.2 38.45 99.3 0.09 13.6 3.7 56129 56050 -3 33.05
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 2.2 38.45 56050 1152 99.2 0.23268 0.2321 0.2293 0.25947 0.254 RANDOM 35.723
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] -0.16 -0.86 0.68 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.921 r_dihedral_angle_4_deg 18.909 r_dihedral_angle_3_deg 14.827 r_dihedral_angle_1_deg 4.655 r_scangle_it 1.589 r_angle_refined_deg 1.136 r_scbond_it 1.08 r_mcangle_it 0.739 r_mcbond_it 0.455 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.921 r_dihedral_angle_4_deg 18.909 r_dihedral_angle_3_deg 14.827 r_dihedral_angle_1_deg 4.655 r_scangle_it 1.589 r_angle_refined_deg 1.136 r_scbond_it 1.08 r_mcangle_it 0.739 r_mcbond_it 0.455 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10271 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 343
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing