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Structure of G9a SET-domain with Histone H3K9M mutant peptide and bound S-adenosylmethionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O8J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 298 0.2 M Tri-ammonium citrate pH 7 and 20% w/v polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.46 50.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.434 α = 90 b = 78.684 β = 90.69 c = 72.769 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 178 CCD ADSC QUANTUM 210 2013-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 1.0010 APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.85 72.76 98.4 14.87 3.8 50405
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 1.85 1.92 97.6 0.637 1.75 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2O8J 1.85 72.76 50405 2700 96.84 0.1993 0.19713 0.2048 0.24 0.2457 RANDOM 46.657
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] -2.83 3.24 1.72 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.998 r_dihedral_angle_4_deg 15.7 r_dihedral_angle_3_deg 13.867 r_long_range_B_refined 9.261 r_long_range_B_other 9.259 r_scangle_other 7.376 r_dihedral_angle_1_deg 6.434 r_mcangle_other 5.482 r_mcangle_it 5.48 r_scbond_it 5.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.998 r_dihedral_angle_4_deg 15.7 r_dihedral_angle_3_deg 13.867 r_long_range_B_refined 9.261 r_long_range_B_other 9.259 r_scangle_other 7.376 r_dihedral_angle_1_deg 6.434 r_mcangle_other 5.482 r_mcangle_it 5.48 r_scbond_it 5.04 r_scbond_other 5.039 r_mcbond_it 4.098 r_mcbond_other 4.096 r_angle_refined_deg 1.757 r_angle_other_deg 1.298 r_chiral_restr 0.111 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.007 r_gen_planes_other 0.007 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4488 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing