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Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DM1 PDB entry 3DM1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 297 14% PEG 3350, 0.2M MgCl2, 0.1M HEPES, pH7.5
, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 1.73 29.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.075 α = 90 b = 40.454 β = 90 c = 53.376 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 IMAGE PLATE RIGAKU RAXIS IV++ VeriMax HR 2009-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.76 50 98.8 0.08 0.08 10.2 6 6339 6339 28.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.76 1.82 89.2 0.473 0.473 1.66 4.1 547
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 (All) 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 3DM1 1.76 24.85 5870 5870 437 98.82 0.21354 0.21354 0.20988 0.2076 0.26634 0.2551 RANDOM 26.219
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] -1.86 -0.69 2.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.611 r_dihedral_angle_3_deg 14.161 r_dihedral_angle_4_deg 13.723 r_dihedral_angle_1_deg 5.914 r_scangle_it 2.999 r_scbond_it 1.939 r_mcangle_it 1.418 r_angle_refined_deg 1.39 r_mcbond_it 0.879 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.611 r_dihedral_angle_3_deg 14.161 r_dihedral_angle_4_deg 13.723 r_dihedral_angle_1_deg 5.914 r_scangle_it 2.999 r_scbond_it 1.939 r_mcangle_it 1.418 r_angle_refined_deg 1.39 r_mcbond_it 0.879 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.187 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.136 r_chiral_restr 0.116 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 521 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement