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High Resolution Structure of Nucleosome Core with Bound Foamy Virus GAG Peptide
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 = 107.168 α = 90 b = 109.638 β = 90 c = 183.557 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 2.17 48.852 98.2 1 20.3 12.2 112248
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 2.17 2.29 0.573
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 2.174 48.852 112016 2303 98.108 0.235 0.2343 0.239 0.2697 0.2694 3 80.065
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] 1.289 -3.34 2.051
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.454 r_dihedral_angle_4_deg 21.897 r_dihedral_angle_3_deg 19.019 r_lrange_it 13.674 r_lrange_other 13.674 r_scangle_it 10.622 r_scangle_other 10.621 r_mcangle_it 7.331 r_mcangle_other 7.33 r_scbond_it 7.263
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.454 r_dihedral_angle_4_deg 21.897 r_dihedral_angle_3_deg 19.019 r_lrange_it 13.674 r_lrange_other 13.674 r_scangle_it 10.622 r_scangle_other 10.621 r_mcangle_it 7.331 r_mcangle_other 7.33 r_scbond_it 7.263 r_scbond_other 7.261 r_dihedral_angle_1_deg 6.28 r_mcbond_it 5.277 r_mcbond_other 5.265 r_angle_refined_deg 1.511 r_angle_other_deg 1.49 r_symmetry_xyhbond_nbd_refined 0.298 r_nbd_other 0.234 r_symmetry_nbd_other 0.214 r_nbd_refined 0.206 r_nbtor_refined 0.206 r_symmetry_nbd_refined 0.185 r_xyhbond_nbd_refined 0.138 r_symmetry_xyhbond_nbd_other 0.093 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.082 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