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Crystal Structure of Nucleosome-H5 Linker Histone Assembly (sticky-169a DNA fragment)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UT9 3UT9, 4QLC experimental model PDB 4QLC 3UT9, 4QLC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Crystal Properties Matthews coefficient Solvent content 2.42 49.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.16 α = 90 b = 103.758 β = 100.97 c = 212.955 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 98.15 PIXEL DECTRIS PILATUS 2M-F 2017-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.84 48.03 98.8 0.999 13.7 6.6 105157
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.84 2.99 92.4 0.421 1 6.1
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 3UT9, 4QLC 2.84 48.03 103041 2096 98.83 0.20155 0.20039 0.2036 0.25898 0.2587 RANDOM 116.381
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] -2.09 0.3 4.51 -2.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.921 r_dihedral_angle_3_deg 19.151 r_dihedral_angle_4_deg 17.954 r_long_range_B_refined 14.31 r_long_range_B_other 14.31 r_scangle_other 10.995 r_mcangle_it 9.046 r_mcangle_other 9.045 r_scbond_it 7.103 r_scbond_other 7.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.921 r_dihedral_angle_3_deg 19.151 r_dihedral_angle_4_deg 17.954 r_long_range_B_refined 14.31 r_long_range_B_other 14.31 r_scangle_other 10.995 r_mcangle_it 9.046 r_mcangle_other 9.045 r_scbond_it 7.103 r_scbond_other 7.103 r_dihedral_angle_1_deg 6.288 r_mcbond_it 5.947 r_mcbond_other 5.947 r_angle_other_deg 1.322 r_angle_refined_deg 1.295 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 13813 Nucleic Acid Atoms 13846 Solvent Atoms 11 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing