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X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer and the two H2A/H2B dimers crosslinked via H2A N38C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KX5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295 Sample was mixed in a 1:1 ratio with 10 mM Na-cacodylate, pH 6.0, 160-210 mM MnCl2, 140-200 mM KCl and equilibrated against a 1:4 dilution of the same solution
Crystal Properties Matthews coefficient Solvent content 2.69 54.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.56 α = 90 b = 183.83 β = 90 c = 109.49 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 90 PIXEL DECTRIS PILATUS 2M-F 2016-06-05 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) 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 2.8 29.505 98.4 0.062 13.9 3.6 52834
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.85 93.7 0.328 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 1kx5 2.8 29.505 1.34 52757 2661 98.34 0.21 0.2076 0.2081 0.2544 0.2503 random
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 31.892 f_angle_d 0.713 f_plane_restr 0.05 f_chiral_restr 0.04 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5956 Nucleic Acid Atoms 6027 Solvent Atoms 62 Heterogen Atoms 24
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing