☰ Navigation Tabs
2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Derivatized with Oxaliplatin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KX4
Crystallization Crystal Properties Matthews coefficient Solvent content 2.56 51.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.001 α = 90 b = 109.436 β = 90 c = 176.357 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 2.6 57 93.5 0.061 18.4 4.5 57610
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 1KX4 2.6 57 57610 1210 93.08 0.26046 0.25999 0.2495 0.2812 0.2703 RANDOM 90.86
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] 2.58 -3.93 1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.277 r_dihedral_angle_4_deg 18.983 r_dihedral_angle_3_deg 18.52 r_dihedral_angle_1_deg 5.098 r_scangle_it 2.159 r_angle_refined_deg 1.433 r_mcangle_it 1.38 r_scbond_it 1.215 r_mcbond_it 0.808 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.277 r_dihedral_angle_4_deg 18.983 r_dihedral_angle_3_deg 18.52 r_dihedral_angle_1_deg 5.098 r_scangle_it 2.159 r_angle_refined_deg 1.433 r_mcangle_it 1.38 r_scbond_it 1.215 r_mcbond_it 0.808 r_nbtor_refined 0.309 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.193 r_symmetry_hbond_refined 0.193 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.077 r_bond_refined_d 0.01 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 6015 Nucleic Acid Atoms 5980 Solvent Atoms Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement