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Crystal Structure of Human Histone-Lysine N-methyltransferase SMYD3 in Complex with S-adenosyl-L-methionine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 293 20% PEG3350, 0.2M Mg Formate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.809 α = 90 b = 65.923 β = 90 c = 108.102 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 315 ROSENBAUM-ROCK HIGH- RESOLUTION DOUBLE-CRYSTAL MONOCHROMATOR 2010-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.1 50 100 0.145 6.4 7.5 26234
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) 2.1 2.18 100 0.423 7.2
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 SAD THROUGHOUT 2.1 44.7 26172 1328 99.7 0.17584 0.174 0.1762 0.208 0.2082 RANDOM 18.78
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] -0.027 0.028 -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.04 r_dihedral_angle_4_deg 17.047 r_dihedral_angle_3_deg 13.559 r_dihedral_angle_1_deg 5.34 r_scangle_it 3.853 r_scbond_it 2.321 r_angle_refined_deg 1.272 r_mcangle_it 1.261 r_mcbond_it 0.628 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.04 r_dihedral_angle_4_deg 17.047 r_dihedral_angle_3_deg 13.559 r_dihedral_angle_1_deg 5.34 r_scangle_it 3.853 r_scbond_it 2.321 r_angle_refined_deg 1.272 r_mcangle_it 1.261 r_mcbond_it 0.628 r_nbtor_refined 0.298 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.166 r_symmetry_hbond_refined 0.126 r_xyhbond_nbd_refined 0.107 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3339 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 30
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling