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X-ray Structure of Human LDHA with an Allosteric Inhibitor (Compound 3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4L4R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M HEPES pH 7.5-7.7, 4-8% PEG 8000, 20% ethylene glycol, and 10% acetonitrile
Crystal Properties Matthews coefficient Solvent content 2.99 58.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.445 α = 90 b = 143.853 β = 90 c = 311.225 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 PILATUS 6M 2015-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.975656 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.91 50 99 0.156 0.995 9.14 4.4 77153
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.91 3.09 96.9 1.078 0.773 1.85 4.6
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 4L4R 2.91 48.8 75038 2100 98.98 0.20848 0.20749 0.2112 0.24447 0.2443 RANDOM 63.2
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] 3.85 0.54 -4.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.647 r_dihedral_angle_4_deg 24.011 r_dihedral_angle_3_deg 17.426 r_long_range_B_other 10.114 r_long_range_B_refined 10.113 r_scangle_other 7.886 r_dihedral_angle_1_deg 6.933 r_mcangle_it 6.851 r_mcangle_other 6.85 r_scbond_it 5.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.647 r_dihedral_angle_4_deg 24.011 r_dihedral_angle_3_deg 17.426 r_long_range_B_other 10.114 r_long_range_B_refined 10.113 r_scangle_other 7.886 r_dihedral_angle_1_deg 6.933 r_mcangle_it 6.851 r_mcangle_other 6.85 r_scbond_it 5.019 r_scbond_other 5 r_mcbond_it 4.515 r_mcbond_other 4.514 r_angle_refined_deg 1.444 r_angle_other_deg 1.165 r_chiral_restr 0.051 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 20320 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 328
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building