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355 bp di-nucleosome harboring cohesive DNA termini (high cryoprotectant)
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 Calcium chloride, Potassium chloride, Potassium Cacodylate, Poly glutamic acid
Crystal Properties Matthews coefficient Solvent content 2.45 49.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.038 α = 90 b = 218.595 β = 90.22 c = 115.931 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 PIXEL DECTRIS PILATUS 2M 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) 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 3.81 48.03 99.8 0.96 0.04 0.999 11.4 6.8 41344
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 3.81 3.96 1.454 0.646 0.424 1.2
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 3.81 48.03 40456 861 99.76 0.2093 0.2077 0.2095 0.2864 0.2816 RANDOM 187.051
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] 0.91 -2.03 -0.03 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.315 r_dihedral_angle_3_deg 18.062 r_dihedral_angle_4_deg 16.765 r_dihedral_angle_1_deg 5.456 r_angle_other_deg 1.382 r_angle_refined_deg 1.266 r_chiral_restr 0.071 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.315 r_dihedral_angle_3_deg 18.062 r_dihedral_angle_4_deg 16.765 r_dihedral_angle_1_deg 5.456 r_angle_other_deg 1.382 r_angle_refined_deg 1.266 r_chiral_restr 0.071 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11934 Nucleic Acid Atoms 14557 Solvent Atoms 1 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing