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Crystal Structure of Nucleosome-H1.0 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 2.47 50.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 208.782 α = 90 b = 102.37 β = 101.12 c = 212.71 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 2017-09-18 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 3.39 48.83 98.9 1 10.5 6.7 122061
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 3.39 3.57 93.4 0.598 1.1 6.7
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 3.39 48.83 119573 2430 98.87 0.22884 0.22741 0.2301 0.29611 0.2902 RANDOM 170.306
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] 2.75 -0.41 1.17 -3.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.352 r_long_range_B_refined 21.907 r_long_range_B_other 21.907 r_dihedral_angle_3_deg 18.809 r_dihedral_angle_4_deg 17.525 r_scangle_other 17.229 r_mcangle_it 15.334 r_mcangle_other 15.334 r_scbond_it 10.898 r_scbond_other 10.898
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.352 r_long_range_B_refined 21.907 r_long_range_B_other 21.907 r_dihedral_angle_3_deg 18.809 r_dihedral_angle_4_deg 17.525 r_scangle_other 17.229 r_mcangle_it 15.334 r_mcangle_other 15.334 r_scbond_it 10.898 r_scbond_other 10.898 r_mcbond_it 9.977 r_mcbond_other 9.974 r_dihedral_angle_1_deg 6.752 r_angle_other_deg 1.367 r_angle_refined_deg 1.303 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 25773 Nucleic Acid Atoms 27692 Solvent Atoms Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing