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Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y245F / H4-Lys20 / AdoHcy
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZKK PDB entry 1ZKK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.39 48.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.99 α = 89.37 b = 45.55 β = 87.09 c = 94.41 γ = 90.5
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 CCD ADSC QUANTUM 270 2005-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 1.0000 ESRF BM30A
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 1.6 40 0.041 31.1 3.6 90904 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.7 0.173 8.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB entry 1ZKK 1.6 38.9 2 87679 4612 100 0.21776 0.21571 0.2372 0.25697 0.2706 RANDOM 8.13
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] -0.04 0.01 0.03 0.01 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.263 r_dihedral_angle_4_deg 16.258 r_dihedral_angle_3_deg 14.173 r_dihedral_angle_1_deg 6.491 r_scangle_it 3.234 r_scbond_it 2.301 r_angle_refined_deg 1.6 r_mcangle_it 1.418 r_mcbond_it 0.981 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.263 r_dihedral_angle_4_deg 16.258 r_dihedral_angle_3_deg 14.173 r_dihedral_angle_1_deg 6.491 r_scangle_it 3.234 r_scbond_it 2.301 r_angle_refined_deg 1.6 r_mcangle_it 1.418 r_mcbond_it 0.981 r_nbtor_refined 0.305 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.198 r_symmetry_hbond_refined 0.137 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.112 r_bond_refined_d 0.016 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5422 Nucleic Acid Atoms Solvent Atoms 589 Heterogen Atoms 104
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling