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Crystal Structure of Protein Lysine Methyltransferase SMYD2 in complex with LLY-507, a Cell-Active, Potent and Selective Inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 281 100 mM Tris HCl pH 8.6, 14% PEG 20K and 200 mM Sodium Chloride
Crystal Properties Matthews coefficient Solvent content 2.64 53.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.025 α = 90 b = 99.92 β = 90 c = 60.297 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-225 2013-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.63 19.7 97.8 9.3 7.5 66084
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.63 19.7 62742 3340 97.47 0.1536 0.15116 0.1581 0.20013 0.2016 RANDOM 23.395
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] 0.62 -0.08 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.013 r_sphericity_free 24.155 r_sphericity_bonded 21.416 r_dihedral_angle_4_deg 16.663 r_dihedral_angle_3_deg 11.212 r_long_range_B_refined 7.477 r_mcangle_it 7.336 r_scbond_it 6.598 r_mcbond_it 6.501 r_dihedral_angle_1_deg 4.856
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.013 r_sphericity_free 24.155 r_sphericity_bonded 21.416 r_dihedral_angle_4_deg 16.663 r_dihedral_angle_3_deg 11.212 r_long_range_B_refined 7.477 r_mcangle_it 7.336 r_scbond_it 6.598 r_mcbond_it 6.501 r_dihedral_angle_1_deg 4.856 r_angle_refined_deg 1.004 r_rigid_bond_restr 0.727 r_chiral_restr 0.07 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 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_it r_scangle_other r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3218 Nucleic Acid Atoms Solvent Atoms 430 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement