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Binding of Nickel 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 2.7 54.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.129 α = 90 b = 109.643 β = 90 c = 183.109 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 1.48 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 2.65 94.07 98.2 0.064 19.7 5.6 61576 60265 79.1
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 2.65 2.79 89.2 0.496 2 4.3 7953
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 2.65 51 60265 1248 98.02 0.23319 0.23229 0.2363 0.27613 0.2745 RANDOM 85.9
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] 2.14 -3.41 1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.255 r_dihedral_angle_4_deg 20.106 r_dihedral_angle_3_deg 18.104 r_dihedral_angle_1_deg 5.158 r_scangle_it 2.25 r_angle_refined_deg 1.498 r_mcangle_it 1.47 r_scbond_it 1.265 r_mcbond_it 0.814 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.255 r_dihedral_angle_4_deg 20.106 r_dihedral_angle_3_deg 18.104 r_dihedral_angle_1_deg 5.158 r_scangle_it 2.25 r_angle_refined_deg 1.498 r_mcangle_it 1.47 r_scbond_it 1.265 r_mcbond_it 0.814 r_nbtor_refined 0.312 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.206 r_xyhbond_nbd_refined 0.151 r_metal_ion_refined 0.148 r_symmetry_hbond_refined 0.081 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6169 Nucleic Acid Atoms 6021 Solvent Atoms Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing