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Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / 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 48.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44 α = 89.2 b = 45.6 β = 87.1 c = 94.2 γ = 90.8
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 MAR CCD 165 mm 2006-02-06 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 1.6 12.84 0.027 38.2 3.9 91908 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 1.65 0.146 10.6
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 12.84 2 87774 4620 100 0.16435 0.16218 0.1619 0.2063 0.2054 RANDOM 16.999
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.842 r_dihedral_angle_4_deg 16.671 r_dihedral_angle_3_deg 11.798 r_dihedral_angle_1_deg 5.951 r_sphericity_free 4.229 r_scangle_it 3.452 r_sphericity_bonded 2.606 r_scbond_it 2.532 r_rigid_bond_restr 1.832 r_mcangle_it 1.623
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.842 r_dihedral_angle_4_deg 16.671 r_dihedral_angle_3_deg 11.798 r_dihedral_angle_1_deg 5.951 r_sphericity_free 4.229 r_scangle_it 3.452 r_sphericity_bonded 2.606 r_scbond_it 2.532 r_rigid_bond_restr 1.832 r_mcangle_it 1.623 r_angle_refined_deg 1.254 r_mcbond_it 1.029 r_nbtor_refined 0.304 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.158 r_xyhbond_nbd_refined 0.13 r_symmetry_hbond_refined 0.124 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5428 Nucleic Acid Atoms Solvent Atoms 1022 Heterogen Atoms 104
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling