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Binding of Cobalt ions to the Nucleosome Core Particle
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KX5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 291 85mM MnCl2, 60mM KCl, 40mM K-cacodylate, pH 6.0, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.72 54.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.502 α = 90 b = 109.94 β = 90 c = 183.352 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 PIXEL PSI PILATUS 6M Dynamically bendable mirror 2009-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.6 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.44 94.49 91.6 0.063 17 4.7 73764 72231 64
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 2.44 2.57 59.5 0.442 1 2.1 6843
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1KX5 2.44 52.6 72231 1466 91.3 0.24022 0.23935 0.28245 0.2889 RANDOM 83.713
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] 1.44 -3.08 1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.484 r_dihedral_angle_4_deg 20.863 r_dihedral_angle_3_deg 17.763 r_dihedral_angle_1_deg 5.909 r_scangle_it 2.127 r_angle_refined_deg 1.433 r_mcangle_it 1.375 r_scbond_it 1.195 r_mcbond_it 0.777 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.484 r_dihedral_angle_4_deg 20.863 r_dihedral_angle_3_deg 17.763 r_dihedral_angle_1_deg 5.909 r_scangle_it 2.127 r_angle_refined_deg 1.433 r_mcangle_it 1.375 r_scbond_it 1.195 r_mcbond_it 0.777 r_nbtor_refined 0.302 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.184 r_xyhbond_nbd_refined 0.145 r_symmetry_hbond_refined 0.099 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6160 Nucleic Acid Atoms 6021 Solvent Atoms Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing