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A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NZD PDB ENTRY 2NZD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 291 55mM KCl, 85mM MnCl2, 20mM K-Cacodylate, pH 6, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.72 54.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.35 α = 90 b = 109.86 β = 90 c = 182.59 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 90 PIXEL PSI PILATUS 6M 2009-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.5 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 2.5 94.13 99.7 0.061 9.7 4.4 74426 72
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) 2.5 2.64 98.2 0.484 1.7 3.5 10557
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 2NZD 2.5 94.13 74426 72837 1485 99.54 0.2475 0.24809 0.24747 0.2404 0.27704 0.2686 RANDOM 85.801
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] 0.77 -2.19 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.261 r_dihedral_angle_4_deg 21.216 r_dihedral_angle_3_deg 17.55 r_dihedral_angle_1_deg 5.085 r_scangle_it 1.979 r_angle_refined_deg 1.475 r_mcangle_it 1.3 r_scbond_it 1.097 r_mcbond_it 0.717 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.261 r_dihedral_angle_4_deg 21.216 r_dihedral_angle_3_deg 17.55 r_dihedral_angle_1_deg 5.085 r_scangle_it 1.979 r_angle_refined_deg 1.475 r_mcangle_it 1.3 r_scbond_it 1.097 r_mcbond_it 0.717 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.219 r_symmetry_vdw_refined 0.213 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.156 r_metal_ion_refined 0.153 r_chiral_restr 0.135 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6086 Nucleic Acid Atoms 5939 Solvent Atoms 22 Heterogen Atoms 79
Software Software Software Name Purpose RemDAq data collection PHASES phasing REFMAC refinement MOSFLM data reduction SCALA data scaling