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Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an 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 2.66 53.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 213.85 α = 90 b = 102.46 β = 100.49 c = 218.289 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 2017-09-17 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 3.506 88.439 100 1 8 6.1 117231
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 3.51 3.57 100 0.37 1.1 5.9
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 3.506 88.439 112443 2266 95.918 0.208 0.2062 0.209 0.2795 0.2757 RANDOM 147.315
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] 0.062 0.533 -2.352 1.958
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.571 r_lrange_it 24.996 r_lrange_other 24.996 r_scangle_it 19.237 r_scangle_other 19.237 r_dihedral_angle_3_deg 19.075 r_dihedral_angle_4_deg 18.325 r_mcangle_other 14.433 r_mcangle_it 14.432 r_scbond_it 12.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.571 r_lrange_it 24.996 r_lrange_other 24.996 r_scangle_it 19.237 r_scangle_other 19.237 r_dihedral_angle_3_deg 19.075 r_dihedral_angle_4_deg 18.325 r_mcangle_other 14.433 r_mcangle_it 14.432 r_scbond_it 12.143 r_scbond_other 12.142 r_mcbond_it 9.497 r_mcbond_other 9.492 r_dihedral_angle_1_deg 6.985 r_angle_other_deg 1.436 r_angle_refined_deg 1.349 r_nbd_other 0.437 r_symmetry_xyhbond_nbd_refined 0.385 r_symmetry_nbd_refined 0.334 r_symmetry_nbd_other 0.216 r_nbtor_refined 0.211 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.16 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.073 r_symmetry_xyhbond_nbd_other 0.071 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 24850 Nucleic Acid Atoms 27724 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing