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Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KX4 NCP146b (pdb code 1KX4)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 Kcacodylate, KCl, MnCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.64 53.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.37 α = 90 b = 109.66 β = 90 c = 175.75 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 PSI PILATUS 6M 2009-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.5 93.04 90.6 0.08 7.8 4.6 65509 65509
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 61.9 0.384 0.384 1.9 2.1 6362
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 NCP146b (pdb code 1KX4) 2.5 93.04 65180 1317 89.97 0.27 0.269 0.2639 0.319 0.3168 RANDOM 109.4
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] 8.93 -9.66 0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.432 r_dihedral_angle_3_deg 21.065 r_dihedral_angle_4_deg 19.248 r_dihedral_angle_1_deg 5.983 r_scangle_it 1.6 r_angle_refined_deg 1.476 r_mcangle_it 1.064 r_scbond_it 0.866 r_mcbond_it 0.589 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.432 r_dihedral_angle_3_deg 21.065 r_dihedral_angle_4_deg 19.248 r_dihedral_angle_1_deg 5.983 r_scangle_it 1.6 r_angle_refined_deg 1.476 r_mcangle_it 1.064 r_scbond_it 0.866 r_mcbond_it 0.589 r_nbtor_refined 0.31 r_symmetry_hbond_refined 0.263 r_nbd_refined 0.223 r_symmetry_vdw_refined 0.193 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5959 Nucleic Acid Atoms 5939 Solvent Atoms Heterogen Atoms 8
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction PHASES phasing