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Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (S,S-configuration)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MNN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 35-55 mM MnCl2, 25-49 mM KCl, 20 mM K-Cacodylate pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.59 52.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.76 α = 90 b = 109.56 β = 90 c = 175.22 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 100 CCD PSI PILATUS 6M 2014-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.5 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.87 70.36 99.8 15.6 5.7 48120
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.87 3.03 99.1 0.498 5.3
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 3MNN 2.87 68.423 47071 981 99.78 0.22774 0.22691 0.2257 0.26574 0.2614 RANDOM 110.569
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] 9.54 -8.44 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.396 r_dihedral_angle_4_deg 20.478 r_dihedral_angle_3_deg 17.177 r_long_range_B_refined 15.144 r_long_range_B_other 15.143 r_scangle_other 10.968 r_mcangle_it 8.162 r_mcangle_other 8.161 r_scbond_it 7.105 r_scbond_other 7.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.396 r_dihedral_angle_4_deg 20.478 r_dihedral_angle_3_deg 17.177 r_long_range_B_refined 15.144 r_long_range_B_other 15.143 r_scangle_other 10.968 r_mcangle_it 8.162 r_mcangle_other 8.161 r_scbond_it 7.105 r_scbond_other 7.1 r_dihedral_angle_1_deg 5.588 r_mcbond_it 5.467 r_mcbond_other 5.462 r_angle_refined_deg 1.413 r_angle_other_deg 1.272 r_chiral_restr 0.195 r_bond_refined_d 0.007 r_bond_other_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.001 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 6094 Nucleic Acid Atoms 5939 Solvent Atoms Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement