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Crystal structure of human chromobox homolog 8 (CBX8) with H3K9 peptide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 298 pH 7.0, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.77 55.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.307 α = 90 b = 51.545 β = 90 c = 77.32 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 225 mm CCD Cryo-cooled first crystal and sagitally focusing second crystal M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.0000 CLSI 08ID-1
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 1.55 50 23019
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.55 50 23019 1180 98.03 0.215 0.213 0.2101 0.249 0.247 RANDOM 19.565
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] 1.22 -0.75 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.388 r_dihedral_angle_4_deg 16.961 r_dihedral_angle_3_deg 14.659 r_dihedral_angle_1_deg 6.51 r_scangle_it 5.756 r_scbond_it 3.8 r_mcangle_it 2.69 r_angle_refined_deg 2.536 r_mcbond_it 1.706 r_chiral_restr 0.175
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.388 r_dihedral_angle_4_deg 16.961 r_dihedral_angle_3_deg 14.659 r_dihedral_angle_1_deg 6.51 r_scangle_it 5.756 r_scbond_it 3.8 r_mcangle_it 2.69 r_angle_refined_deg 2.536 r_mcbond_it 1.706 r_chiral_restr 0.175 r_bond_refined_d 0.029 r_gen_planes_refined 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 946 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing