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Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Kaposi Sarcoma Associated Herpesvirus LANA Peptide-Au[I] Compound)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IPU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Crystal Properties Matthews coefficient Solvent content 3.06 59.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.105 α = 90 b = 109.609 β = 90 c = 183.767 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 PIXEL DECTRIS PILATUS 2M-F 2018-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.04 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.3 48.93 99.9 1 27.3 12.2 97275
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.43 0.651
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.301 48.93 97189 1952 99.832 0.224 0.2235 0.2263 0.2623 0.2621 3 94.074
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] 4.758 -4.784 0.026
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.82 r_dihedral_angle_4_deg 21.142 r_dihedral_angle_3_deg 18.892 r_lrange_it 15.477 r_lrange_other 15.477 r_scangle_it 12.244 r_scangle_other 12.243 r_mcangle_other 8.629 r_mcangle_it 8.628 r_scbond_it 8.289
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.82 r_dihedral_angle_4_deg 21.142 r_dihedral_angle_3_deg 18.892 r_lrange_it 15.477 r_lrange_other 15.477 r_scangle_it 12.244 r_scangle_other 12.243 r_mcangle_other 8.629 r_mcangle_it 8.628 r_scbond_it 8.289 r_scbond_other 8.288 r_dihedral_angle_1_deg 6.272 r_mcbond_it 6.176 r_mcbond_other 6.173 r_angle_other_deg 2.441 r_angle_refined_deg 1.474 r_symmetry_nbd_other 0.242 r_symmetry_xyhbond_nbd_refined 0.21 r_nbtor_refined 0.207 r_nbd_refined 0.205 r_nbd_other 0.198 r_symmetry_nbd_refined 0.155 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.076 r_bond_other_d 0.028 r_gen_planes_other 0.013 r_gen_planes_refined 0.008 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6215 Nucleic Acid Atoms 5939 Solvent Atoms Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing