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169 bp nucleosome harboring non-identical cohesive DNA termini.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UT9
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 2.71 54.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.338 α = 61.5 b = 116.545 β = 82.77 c = 117.9 γ = 64.23
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 3 48.12 98.6 0.056 0.079 0.056 0.997 12 3.5 88754
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.05 93.7 0.883 0.883 0.539 1 3.1
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 3 48.12 86975 1778 98.6 0.2094 0.2084 0.2108 0.2609 0.2583 RANDOM 118.078
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] 1.67 -2.53 0.73 -2.66 1.91 1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.959 r_dihedral_angle_3_deg 18.971 r_dihedral_angle_4_deg 17.584 r_dihedral_angle_1_deg 6.033 r_angle_other_deg 2.321 r_angle_refined_deg 1.152 r_chiral_restr 0.063 r_bond_other_d 0.027 r_gen_planes_refined 0.005 r_gen_planes_other 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.959 r_dihedral_angle_3_deg 18.971 r_dihedral_angle_4_deg 17.584 r_dihedral_angle_1_deg 6.033 r_angle_other_deg 2.321 r_angle_refined_deg 1.152 r_chiral_restr 0.063 r_bond_other_d 0.027 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_refined_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12007 Nucleic Acid Atoms 13862 Solvent Atoms 25 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction Aimless data scaling MOLREP phasing