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Crystal structure of SMYD3 with SAM and oxindole compound
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.10 M Magnesium formate, 0.1M Tris 8.0, 14% w/v PEG 3350. Crystals of SMYD3-SAM were produced and compound was soaked into the pre-formed crystals
Crystal Properties Matthews coefficient Solvent content 2.07 40.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.594 α = 90 b = 65.232 β = 90 c = 105.966 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 CCD ADSC QUANTUM 315r 2014-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97907 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.5 55.55 94.4 0.069 0.077 0.033 14.6 5 62186
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.55 98.6 0.226 0.253 0.111 0.948 4.9 6399
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 1.5 55.55 59053 3081 94.29 0.1159 0.1134 0.113 0.1643 0.1646 RANDOM 22.997
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] 0.61 -0.56 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.614 r_sphericity_free 23.573 r_dihedral_angle_4_deg 19.865 r_dihedral_angle_3_deg 14.196 r_sphericity_bonded 11.646 r_dihedral_angle_1_deg 6.11 r_mcangle_it 3.787 r_mcbond_it 3.367 r_mcbond_other 3.367 r_rigid_bond_restr 3.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.614 r_sphericity_free 23.573 r_dihedral_angle_4_deg 19.865 r_dihedral_angle_3_deg 14.196 r_sphericity_bonded 11.646 r_dihedral_angle_1_deg 6.11 r_mcangle_it 3.787 r_mcbond_it 3.367 r_mcbond_other 3.367 r_rigid_bond_restr 3.323 r_angle_refined_deg 1.732 r_angle_other_deg 0.913 r_chiral_restr 0.124 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3400 Nucleic Acid Atoms Solvent Atoms 449 Heterogen Atoms 73
Software Software Software Name Purpose HKL-2000 data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction