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Structure of a nucleosome composed of a palindromic 167-base pair blunt-ended 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 MnCl2-containing buffers
Crystal Properties Matthews coefficient Solvent content 2.76 55.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.437 α = 90 b = 103.722 β = 93.59 c = 185.405 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 100 PIXEL DECTRIS PILATUS 2M-F 2014-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.9 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 3.26 48.66 96 0.997 8.9 3.2 61655
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 3.26 3.44 0.541
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 3.261 48.655 57291 2865 89.061 0.272 0.2692 0.2711 0.321 0.3196 88.517
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] -2.504 -0.466 -1.818 4.346
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.49 r_dihedral_angle_3_deg 16.373 r_dihedral_angle_4_deg 15.954 r_lrange_it 7.703 r_lrange_other 7.703 r_dihedral_angle_1_deg 5.064 r_scangle_it 4.717 r_scangle_other 4.716 r_mcangle_it 4.115 r_mcangle_other 4.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.49 r_dihedral_angle_3_deg 16.373 r_dihedral_angle_4_deg 15.954 r_lrange_it 7.703 r_lrange_other 7.703 r_dihedral_angle_1_deg 5.064 r_scangle_it 4.717 r_scangle_other 4.716 r_mcangle_it 4.115 r_mcangle_other 4.115 r_scbond_it 2.758 r_scbond_other 2.758 r_mcbond_it 2.351 r_mcbond_other 2.351 r_angle_other_deg 2.296 r_angle_refined_deg 1.232 r_symmetry_nbd_refined 0.264 r_nbd_other 0.249 r_symmetry_nbd_other 0.222 r_nbtor_refined 0.211 r_nbd_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.165 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.075 r_symmetry_xyhbond_nbd_other 0.045 r_bond_other_d 0.027 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11980 Nucleic Acid Atoms 13682 Solvent Atoms Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing