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DNA Stretching in the Nucleosome Facilitates Alkylation by an Intercalating Antitumor Agent
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 EVAPORATION 6 291 85 mM MnCl2, 60 mM KCl, 20 mM K-Cacodylate, 4 mg/ml NCP over well with 1/2 conc., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K, EVAPORATION
Crystal Properties Matthews coefficient Solvent content 2.7 54.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.161 α = 90 b = 109.588 β = 90 c = 182.413 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 IMAGE PLATE RIGAKU RAXIS IV M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54180
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 2.9 54.8 99.9 0.068 7.4 47896
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) 2.9 3.06 99.2 0.483 2.9 5.3 6839
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 PDB ENTRY 2NZD 2.9 53.17 46854 978 99.86 0.23896 0.238 0.2255 0.28591 0.2718 RANDOM 76.089
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] 2.12 -3.16 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.19 r_dihedral_angle_4_deg 20.053 r_dihedral_angle_3_deg 18.419 r_dihedral_angle_1_deg 4.901 r_scangle_it 1.855 r_angle_refined_deg 1.389 r_mcangle_it 1.08 r_scbond_it 0.99 r_mcbond_it 0.605 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.19 r_dihedral_angle_4_deg 20.053 r_dihedral_angle_3_deg 18.419 r_dihedral_angle_1_deg 4.901 r_scangle_it 1.855 r_angle_refined_deg 1.389 r_mcangle_it 1.08 r_scbond_it 0.99 r_mcbond_it 0.605 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.3 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.181 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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_refined 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 6064 Nucleic Acid Atoms 5939 Solvent Atoms Heterogen Atoms 39
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement MOSFLM data reduction