☰ Navigation Tabs
Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,R-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 52.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.19 α = 90 b = 109.4 β = 90 c = 174.82 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 2014-10-09 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 2.6 58.27 99.9 15 5.8 64455
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 2.6 2.67 99.6 0.505 5.4
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 2.6 52.748 63050 1303 99.8 0.23534 0.23458 0.2346 0.27017 0.2662 RANDOM 105.554
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] 9.65 -7.35 -2.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.454 r_dihedral_angle_4_deg 20.623 r_dihedral_angle_3_deg 17.142 r_long_range_B_refined 16.016 r_long_range_B_other 16.015 r_scangle_other 11.892 r_mcangle_it 8.156 r_mcangle_other 8.155 r_scbond_it 7.899 r_scbond_other 7.895
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.454 r_dihedral_angle_4_deg 20.623 r_dihedral_angle_3_deg 17.142 r_long_range_B_refined 16.016 r_long_range_B_other 16.015 r_scangle_other 11.892 r_mcangle_it 8.156 r_mcangle_other 8.155 r_scbond_it 7.899 r_scbond_other 7.895 r_dihedral_angle_1_deg 5.761 r_mcbond_it 5.707 r_mcbond_other 5.699 r_angle_refined_deg 1.452 r_angle_other_deg 1.292 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 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