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Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me1 / 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 48.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.4 α = 91.4 b = 45 β = 115.3 c = 52.4 γ = 89.8
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 MARMOSAIC 300 mm CCD 2006-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
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 1.5 25 0.067 22.5 7.8 55907 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 1.5 1.6 0.528 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 1.5 23.68 2 53407 2811 100 0.19497 0.19364 0.1842 0.22012 0.2129 RANDOM 32.444
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] -0.25 -0.05 0.1 0.21 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.569 r_dihedral_angle_4_deg 17.717 r_dihedral_angle_3_deg 14.017 r_dihedral_angle_1_deg 6.543 r_scangle_it 4.082 r_scbond_it 2.794 r_angle_refined_deg 1.895 r_mcangle_it 1.862 r_mcbond_it 1.216 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.569 r_dihedral_angle_4_deg 17.717 r_dihedral_angle_3_deg 14.017 r_dihedral_angle_1_deg 6.543 r_scangle_it 4.082 r_scbond_it 2.794 r_angle_refined_deg 1.895 r_mcangle_it 1.862 r_mcbond_it 1.216 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.235 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.205 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.123 r_bond_refined_d 0.019 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2680 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 52
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling