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Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Foamy Virus GAG 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 3.02 59.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.194 α = 90 b = 109.563 β = 90 c = 183.675 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 2.6 48.83 93.6 0.999 19.6 12.5 62688
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 2.6 2.74 0.567
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 2.604 48.828 62632 1262 93.594 0.214 0.2126 0.2152 0.2619 0.2634 3 95.165
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] 1.614 -5.844 4.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.291 r_dihedral_angle_4_deg 21.496 r_dihedral_angle_3_deg 19.94 r_lrange_it 17.955 r_lrange_other 17.955 r_scangle_it 14.741 r_scangle_other 14.74 r_scbond_it 9.86 r_scbond_other 9.86 r_mcangle_it 9.844
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.291 r_dihedral_angle_4_deg 21.496 r_dihedral_angle_3_deg 19.94 r_lrange_it 17.955 r_lrange_other 17.955 r_scangle_it 14.741 r_scangle_other 14.74 r_scbond_it 9.86 r_scbond_other 9.86 r_mcangle_it 9.844 r_mcangle_other 9.844 r_mcbond_it 6.948 r_mcbond_other 6.942 r_dihedral_angle_1_deg 6.776 r_angle_refined_deg 1.62 r_angle_other_deg 1.484 r_symmetry_xyhbond_nbd_refined 0.46 r_symmetry_nbd_other 0.221 r_nbd_refined 0.219 r_nbd_other 0.217 r_nbtor_refined 0.211 r_symmetry_nbd_refined 0.199 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.084 r_xyhbond_nbd_other 0.084 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.069 r_metal_ion_refined 0.018 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6257 Nucleic Acid Atoms 5939 Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing