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Crystal structure of a ternary complex of the methyltransferase SET9 (also known as SET7/9) with a P53 peptide and SAH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O9S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.8 291 PEG3350, Tris-HCL, pH 7.8, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.46 49.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.374 α = 90 b = 103.123 β = 90.04 c = 67.165 γ = 90
Symmetry Space Group P 1 21 1
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 4 2003-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 0.978 SRS PX14.2
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 1.75 20 94.7 0.038 24.8 15 55234 52283 3 3 27.7
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) 1.75 1.81 67.6 0.378 2.5 3706
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1o9s 1.75 20 52262 49595 2667 94.72 0.18571 0.18371 0.2272 0.22325 0.2523 RANDOM 7.381
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] -1.62 0.65 0.28 1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.846 r_dihedral_angle_1_deg 4.536 r_scangle_it 2.314 r_angle_refined_deg 1.753 r_angle_other_deg 1.732 r_scbond_it 1.429 r_mcangle_it 1.058 r_sphericity_free 0.952 r_rigid_bond_restr 0.887 r_sphericity_bonded 0.577
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.846 r_dihedral_angle_1_deg 4.536 r_scangle_it 2.314 r_angle_refined_deg 1.753 r_angle_other_deg 1.732 r_scbond_it 1.429 r_mcangle_it 1.058 r_sphericity_free 0.952 r_rigid_bond_restr 0.887 r_sphericity_bonded 0.577 r_mcbond_it 0.551 r_nbtor_other 0.292 r_nbd_refined 0.268 r_symmetry_vdw_refined 0.243 r_nbd_other 0.241 r_symmetry_vdw_other 0.233 r_symmetry_hbond_refined 0.215 r_xyhbond_nbd_refined 0.182 r_chiral_restr 0.166 r_xyhbond_nbd_other 0.078 r_symmetry_hbond_other 0.024 r_bond_refined_d 0.01 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_bond_other_d r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_metal_ion_refined r_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4002 Nucleic Acid Atoms Solvent Atoms 717 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing