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Crystal Structure of Nucleosome-H1x Linker Histone Assembly (sticky-169a DNA fragment)
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 291 40-45 mM CaCl2, 25 mM KCl, 10 mM Na-acetate (pH 4.5)
Crystal Properties Matthews coefficient Solvent content 2.43 49.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.852 α = 90 b = 102.111 β = 96.337 c = 216.179 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-F 2015-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00 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 2.7 92.22 99.6 0.998 9.8 3.4 124272
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 2.7 2.85 0.521
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.7 92.22 124251 2402 99.562 0.211 0.2096 0.2124 0.2669 0.2681 88.021
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] -2.576 0.622 -1.286 3.634
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.684 r_dihedral_angle_3_deg 19.796 r_dihedral_angle_4_deg 18.479 r_lrange_it 10.573 r_lrange_other 10.567 r_scangle_it 7.637 r_scangle_other 7.637 r_dihedral_angle_1_deg 6.598 r_mcangle_it 6.48 r_mcangle_other 6.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.684 r_dihedral_angle_3_deg 19.796 r_dihedral_angle_4_deg 18.479 r_lrange_it 10.573 r_lrange_other 10.567 r_scangle_it 7.637 r_scangle_other 7.637 r_dihedral_angle_1_deg 6.598 r_mcangle_it 6.48 r_mcangle_other 6.48 r_scbond_it 4.929 r_scbond_other 4.929 r_mcbond_it 4.192 r_mcbond_other 4.191 r_angle_other_deg 1.334 r_angle_refined_deg 1.229 r_symmetry_nbd_refined 0.285 r_nbd_other 0.271 r_symmetry_xyhbond_nbd_refined 0.233 r_symmetry_nbd_other 0.213 r_nbtor_refined 0.204 r_metal_ion_refined 0.203 r_nbd_refined 0.186 r_xyhbond_nbd_refined 0.165 r_symmetry_metal_ion_refined 0.152 r_symmetry_nbtor_other 0.075 r_symmetry_xyhbond_nbd_other 0.069 r_chiral_restr 0.066 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14012 Nucleic Acid Atoms 13846 Solvent Atoms 157 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing