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Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me2 / 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 2.42 49.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.112 α = 89.45 b = 45.742 β = 87.59 c = 94.76 γ = 89.9
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 MAR CCD 165 mm 2005-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-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 1.25 50 0.028 30.4 2.9 204489 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) 1.25 1.29 0.131 9.9
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 1.25 47.35 2 183160 9694 94.31 0.18238 0.18104 0.1866 0.2073 0.2126 RANDOM 16.883
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] 0.03 0.01 0.05 0.01 -0.06 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.063 r_dihedral_angle_4_deg 15.232 r_dihedral_angle_3_deg 11.835 r_dihedral_angle_1_deg 6.234 r_scangle_it 4.731 r_scbond_it 3.691 r_mcangle_it 2.478 r_mcbond_it 2.072 r_angle_refined_deg 1.573 r_mcbond_other 1.451
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.063 r_dihedral_angle_4_deg 15.232 r_dihedral_angle_3_deg 11.835 r_dihedral_angle_1_deg 6.234 r_scangle_it 4.731 r_scbond_it 3.691 r_mcangle_it 2.478 r_mcbond_it 2.072 r_angle_refined_deg 1.573 r_mcbond_other 1.451 r_angle_other_deg 0.881 r_symmetry_vdw_other 0.247 r_nbd_refined 0.228 r_nbd_other 0.216 r_symmetry_hbond_refined 0.182 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.159 r_symmetry_vdw_refined 0.149 r_chiral_restr 0.097 r_nbtor_other 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5441 Nucleic Acid Atoms Solvent Atoms 864 Heterogen Atoms 104
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling