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RAPTA-B (Ruthenium[II]-benzene-phosphaadamantane) cancer drug binding to the nucleosome core
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MNN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 55 mM KCl, 85 mM MnCl2, 20 mM K-Cacodylate (pH 6.0)
Crystal Properties Matthews coefficient Solvent content 2.7 54.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.682 α = 90 b = 110.006 β = 90 c = 182.426 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 DECTRIS PILATUS 2M 2012-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.5 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.75 48.89 99.6 1 20.1 6 56299
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.9 0.447
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.75 48.89 56236 1182 99.517 0.221 0.2202 0.2209 0.2688 0.2111 115.258
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] 0.324 -5.092 4.768
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.339 r_lrange_it 16.297 r_lrange_other 16.297 r_dihedral_angle_6_deg 15.583 r_scangle_it 12.516 r_scangle_other 12.516 r_mcangle_it 8.79 r_mcangle_other 8.789 r_scbond_it 8.078 r_scbond_other 8.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.339 r_lrange_it 16.297 r_lrange_other 16.297 r_dihedral_angle_6_deg 15.583 r_scangle_it 12.516 r_scangle_other 12.516 r_mcangle_it 8.79 r_mcangle_other 8.789 r_scbond_it 8.078 r_scbond_other 8.078 r_mcbond_it 6.036 r_mcbond_other 6.029 r_dihedral_angle_1_deg 5.532 r_dihedral_angle_2_deg 5.437 r_angle_refined_deg 1.384 r_dihedral_angle_other_2_deg 0.82 r_angle_other_deg 0.44 r_nbtor_refined 0.214 r_symmetry_nbd_other 0.211 r_nbd_refined 0.205 r_symmetry_xyhbond_nbd_refined 0.198 r_symmetry_nbd_refined 0.168 r_xyhbond_nbd_refined 0.156 r_nbd_other 0.155 r_symmetry_xyhbond_nbd_other 0.108 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.056 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6086 Nucleic Acid Atoms 5939 Solvent Atoms Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing