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169 bp nucleosome, harboring cohesive DNA termini, assembled 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 Calcium chloride, potassium chloride, sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.48 50.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.799 α = 90 b = 102.76 β = 97.4 c = 218.05 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 2015-09-18 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) 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 3.2 216.23 99.3 0.108 0.151 0.105 0.993 5.3 3 75580
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.37 96.6 0.811 0.557 1.2 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 (All) 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 3.2 39.892 75562 1469 99.242 0.202 0.201 0.2062 0.2619 0.2615 RANDOM 115.807
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] -4.512 4.868 -3.039 6.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.27 r_dihedral_angle_3_deg 19.03 r_dihedral_angle_4_deg 17.077 r_lrange_it 16.931 r_lrange_other 16.931 r_scangle_it 13.096 r_scangle_other 13.095 r_mcangle_it 10.924 r_mcangle_other 10.924 r_scbond_it 8.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.27 r_dihedral_angle_3_deg 19.03 r_dihedral_angle_4_deg 17.077 r_lrange_it 16.931 r_lrange_other 16.931 r_scangle_it 13.096 r_scangle_other 13.095 r_mcangle_it 10.924 r_mcangle_other 10.924 r_scbond_it 8.316 r_scbond_other 8.316 r_mcbond_it 7.1 r_mcbond_other 7.098 r_dihedral_angle_1_deg 6.833 r_angle_other_deg 1.392 r_angle_refined_deg 1.289 r_symmetry_xyhbond_nbd_refined 0.369 r_nbd_other 0.334 r_symmetry_nbd_refined 0.314 r_nbtor_refined 0.207 r_symmetry_nbd_other 0.206 r_nbd_refined 0.19 r_metal_ion_refined 0.162 r_xyhbond_nbd_refined 0.148 r_xyhbond_nbd_other 0.128 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.067 r_symmetry_xyhbond_nbd_other 0.056 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13379 Nucleic Acid Atoms 13846 Solvent Atoms Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling PHASER phasing