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Human nucleosome core particle with cohesive end DNA termini
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NZD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291.15 manganese chloride, potassium chloride, potassium cacodylate
Crystal Properties Matthews coefficient Solvent content 2.98 58.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.31 α = 90 b = 109.66 β = 90 c = 183.819 γ = 90
Symmetry Space Group P 21 21 21
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 2017-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.25 94.18 99.7 0.03 0.997 12.2 11.5 101214
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.37 0.76
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 2NZD 2.25 92.08 99086 2022 99.6 0.23975 0.23868 0.2389 0.29225 0.2935 RANDOM 78.326
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] 5.45 -5.5 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.331 r_dihedral_angle_3_deg 19.571 r_dihedral_angle_4_deg 18.65 r_long_range_B_refined 13.424 r_long_range_B_other 13.424 r_scangle_other 10.415 r_mcangle_it 7.355 r_mcangle_other 7.354 r_scbond_it 7.245 r_scbond_other 7.245
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.331 r_dihedral_angle_3_deg 19.571 r_dihedral_angle_4_deg 18.65 r_long_range_B_refined 13.424 r_long_range_B_other 13.424 r_scangle_other 10.415 r_mcangle_it 7.355 r_mcangle_other 7.354 r_scbond_it 7.245 r_scbond_other 7.245 r_dihedral_angle_1_deg 6.379 r_mcbond_it 5.08 r_mcbond_other 5.08 r_angle_refined_deg 1.496 r_angle_other_deg 1.458 r_chiral_restr 0.08 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6129 Nucleic Acid Atoms 6029 Solvent Atoms 52 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing