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Nucleosome core particle treated with oxaliplatin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KX5 PDB entry 1KX5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 291 MnCl2, KCl, K-Cacodylate, pH 6.0, vapor diffusion, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.66 53.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.298 α = 90 b = 109.655 β = 90 c = 181.807 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 98 CCD MARMOSAIC 225 mm CCD 2007-02-10 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.072 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 3.45 94.072 98.9 0.071 0.071 6.3 7.3 28350 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.45 3.64 100 0.485 0.485 1.5 7.5 4118
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 THROUGHOUT PDB entry 1KX5 3.45 94.07 28295 593 98.73 0.341 0.339 0.3131 0.435 0.3809 RANDOM 190.681
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 -18.23 16.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.924 r_dihedral_angle_3_deg 20.885 r_dihedral_angle_4_deg 17.233 r_dihedral_angle_1_deg 6.642 r_angle_refined_deg 1.276 r_mcangle_it 1.27 r_scangle_it 1.201 r_mcbond_it 0.698 r_scbond_it 0.653 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.924 r_dihedral_angle_3_deg 20.885 r_dihedral_angle_4_deg 17.233 r_dihedral_angle_1_deg 6.642 r_angle_refined_deg 1.276 r_mcangle_it 1.27 r_scangle_it 1.201 r_mcbond_it 0.698 r_scbond_it 0.653 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.25 r_symmetry_hbond_refined 0.237 r_nbd_refined 0.225 r_xyhbond_nbd_refined 0.208 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6269 Nucleic Acid Atoms 6021 Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction