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Structure of Nucleosome Core with a Bound Kaposi Sarcoma Associated Herpesvirus LANA Peptide Having a Methionine to Ornithine Substitution
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 3.13 60.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.714 α = 90 b = 109.882 β = 90 c = 184.88 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 2017-09-18 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 2.5 49.174 99.8 1 23 13.3 77598
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 2.5 2.64 0.667
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 2.503 49.174 77518 1513 99.785 0.219 0.2185 0.2197 0.268 0.2679 3 108.361
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] -6.421 8.006 -1.585
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.323 r_dihedral_angle_4_deg 21.599 r_dihedral_angle_3_deg 19.066 r_lrange_it 17.905 r_lrange_other 17.905 r_scangle_it 14.571 r_scangle_other 14.571 r_mcangle_it 10.362 r_mcangle_other 10.361 r_scbond_it 9.887
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.323 r_dihedral_angle_4_deg 21.599 r_dihedral_angle_3_deg 19.066 r_lrange_it 17.905 r_lrange_other 17.905 r_scangle_it 14.571 r_scangle_other 14.571 r_mcangle_it 10.362 r_mcangle_other 10.361 r_scbond_it 9.887 r_scbond_other 9.887 r_mcbond_it 7.636 r_mcbond_other 7.622 r_dihedral_angle_1_deg 6.401 r_angle_refined_deg 1.515 r_angle_other_deg 1.466 r_symmetry_xyhbond_nbd_refined 0.326 r_nbd_other 0.256 r_symmetry_nbd_other 0.218 r_nbd_refined 0.21 r_nbtor_refined 0.208 r_xyhbond_nbd_refined 0.163 r_symmetry_nbd_refined 0.16 r_symmetry_xyhbond_nbd_other 0.112 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.082 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_xyhbond_nbd_other 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6215 Nucleic Acid Atoms 5939 Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing