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Binding of Rubidium 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 2.69 54.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.462 α = 90 b = 109.681 β = 90 c = 182.213 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 MARMOSAIC 225 mm CCD vertically collimating mirror 2009-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.81 SLS X06DA
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 2.3 94.07 90.3 0.05 21.1 6.7 85891 84087 44.1
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 2.3 2.42 58.6 0.478 3.2 4.6 7966
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 1KX5 2.3 60 84087 1740 90.04 0.24242 0.24191 0.2399 0.26735 0.2625 RANDOM 60.23
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] 0.93 -3.12 2.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.11 r_dihedral_angle_4_deg 20.759 r_dihedral_angle_3_deg 15.624 r_dihedral_angle_1_deg 5.735 r_scangle_it 2.223 r_angle_refined_deg 1.472 r_mcangle_it 1.449 r_scbond_it 1.307 r_mcbond_it 0.839 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.11 r_dihedral_angle_4_deg 20.759 r_dihedral_angle_3_deg 15.624 r_dihedral_angle_1_deg 5.735 r_scangle_it 2.223 r_angle_refined_deg 1.472 r_mcangle_it 1.449 r_scbond_it 1.307 r_mcbond_it 0.839 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.204 r_nbd_refined 0.188 r_xyhbond_nbd_refined 0.139 r_symmetry_hbond_refined 0.092 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6156 Nucleic Acid Atoms 6021 Solvent Atoms Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing