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2.5 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 145 bp Alpha-Satellite DNA (NCP145)
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 6 289 KCl, MnCl2, K-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.67 53.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.606 α = 90 b = 110.066 β = 90 c = 181.719 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 100 CCD MARMOSAIC 225 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.07 SLS X06SA
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 2.5 91 99.6 0.059 21.6 6.9 72054
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2.5 91 72054 72054 1468 99.48 0.23701 0.23634 0.2321 0.26972 0.2664 RANDOM 64.07
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] 2.45 -1.85 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.549 r_dihedral_angle_4_deg 21.223 r_dihedral_angle_3_deg 17.061 r_dihedral_angle_1_deg 5.114 r_scangle_it 2.131 r_angle_refined_deg 1.42 r_mcangle_it 1.302 r_scbond_it 1.2 r_mcbond_it 0.747 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.549 r_dihedral_angle_4_deg 21.223 r_dihedral_angle_3_deg 17.061 r_dihedral_angle_1_deg 5.114 r_scangle_it 2.131 r_angle_refined_deg 1.42 r_mcangle_it 1.302 r_scbond_it 1.2 r_mcbond_it 0.747 r_nbtor_refined 0.306 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.152 r_symmetry_hbond_refined 0.152 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6086 Nucleic Acid Atoms 5939 Solvent Atoms 147 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement