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Human nucleosome core particle containing 145 bp of DNA
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 6 291.15 manganese chloride, potassium chloride, potassium cacodylate
Crystal Properties Matthews coefficient Solvent content 3.07 59.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.56 α = 90 b = 109.71 β = 90 c = 183.48 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 98.15 PIXEL DECTRIS PILATUS 2M-F 2017-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) 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 1.99 94.16 99.6 0.021 0.997 17.4 12.2 148453
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.1 97.9 0.652 0.526 1.3 11.6
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 2NZD 1.99 94.16 145312 3035 99.6 0.237 0.236 0.2417 0.263 0.2664 RANDOM 74.55
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] 1.76 -3.11 1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.301 r_dihedral_angle_4_deg 21.693 r_dihedral_angle_3_deg 16.771 r_long_range_B_other 10.008 r_long_range_B_refined 10.006 r_scangle_other 6.308 r_dihedral_angle_1_deg 5.191 r_mcangle_it 4.56 r_mcangle_other 4.56 r_scbond_it 4.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.301 r_dihedral_angle_4_deg 21.693 r_dihedral_angle_3_deg 16.771 r_long_range_B_other 10.008 r_long_range_B_refined 10.006 r_scangle_other 6.308 r_dihedral_angle_1_deg 5.191 r_mcangle_it 4.56 r_mcangle_other 4.56 r_scbond_it 4.022 r_scbond_other 4.022 r_mcbond_it 3.042 r_mcbond_other 3.041 r_angle_refined_deg 1.474 r_angle_other_deg 1.426 r_chiral_restr 0.2 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6117 Nucleic Acid Atoms 5939 Solvent Atoms 114 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing