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353 bp di-nucleosome harboring cohesive DNA termini with linker histone H1.0
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 4.5 291.15 potassium acetate, calcium chloride, potassium chloride
Crystal Properties Matthews coefficient Solvent content 2.45 49.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.215 α = 86.59 b = 105.053 β = 88.95 c = 171.126 γ = 88.25
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 2019-08-26 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) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.86 49.35 97.4 0.091 0.108 0.057 0.996 7.7 3.4 103522
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.86 2.91 82.9 1.521 1.858 1.046 0.401 0.8 2.8
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 3UT9, 4QLC 2.86 49.35 101413 2099 97.38 0.2264 0.2249 0.23 0.2971 0.298 RANDOM 117.474
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] -5.95 0.03 3.46 -0.27 -4.52 5.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.513 r_dihedral_angle_3_deg 19.868 r_dihedral_angle_4_deg 18.704 r_dihedral_angle_1_deg 6.9 r_angle_refined_deg 1.445 r_angle_other_deg 1.414 r_chiral_restr 0.081 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.513 r_dihedral_angle_3_deg 19.868 r_dihedral_angle_4_deg 18.704 r_dihedral_angle_1_deg 6.9 r_angle_refined_deg 1.445 r_angle_other_deg 1.414 r_chiral_restr 0.081 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13289 Nucleic Acid Atoms 14475 Solvent Atoms 9 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing