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2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KX4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.58 52.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.067 α = 90 b = 109.374 β = 90 c = 176.465 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 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 2.55 93 91.6 0.079 17.5 6.5 60540
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1KX4 2.55 92.85 60540 1253 91.39 0.2343 0.23372 0.2624 0.2627 RANDOM 70.538
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] 0.47 -1.77 1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.091 r_dihedral_angle_4_deg 19.075 r_dihedral_angle_3_deg 18.408 r_dihedral_angle_1_deg 5.175 r_scangle_it 2.023 r_angle_refined_deg 1.432 r_mcangle_it 1.285 r_scbond_it 1.138 r_mcbond_it 0.729 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.091 r_dihedral_angle_4_deg 19.075 r_dihedral_angle_3_deg 18.408 r_dihedral_angle_1_deg 5.175 r_scangle_it 2.023 r_angle_refined_deg 1.432 r_mcangle_it 1.285 r_scbond_it 1.138 r_mcbond_it 0.729 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.213 r_nbd_refined 0.212 r_symmetry_hbond_refined 0.208 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.074 r_symmetry_metal_ion_refined 0.043 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_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 6015 Nucleic Acid Atoms 5980 Solvent Atoms 390 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement