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RAPTA-3IB (Ruthenium[II]-1,3,5-triisopropylbenzene-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 6 291 55 mM KCl, 85 mM MnCl2, 20 mM K-Cacodylate (pH 6.0)
Crystal Properties Matthews coefficient Solvent content 2.7 54.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.78 α = 90 b = 109.9 β = 90 c = 182.34 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 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 2.7 76.58 86.4 0.986 8.6 5.2 51390
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 2.7 2.85 0.492
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 2.7 76.58 51336 1046 86.058 0.232 0.2304 0.2318 0.2913 0.233 102.191
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] 4.494 -6.014 1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.17 r_dihedral_angle_6_deg 15.367 r_lrange_it 14.926 r_lrange_other 14.925 r_scangle_it 11.023 r_scangle_other 11.023 r_mcangle_it 7.719 r_mcangle_other 7.718 r_scbond_it 6.992 r_scbond_other 6.992
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.17 r_dihedral_angle_6_deg 15.367 r_lrange_it 14.926 r_lrange_other 14.925 r_scangle_it 11.023 r_scangle_other 11.023 r_mcangle_it 7.719 r_mcangle_other 7.718 r_scbond_it 6.992 r_scbond_other 6.992 r_dihedral_angle_1_deg 5.675 r_dihedral_angle_2_deg 5.416 r_mcbond_it 5.025 r_mcbond_other 5.021 r_angle_refined_deg 1.352 r_dihedral_angle_other_2_deg 0.828 r_angle_other_deg 0.432 r_symmetry_xyhbond_nbd_refined 0.243 r_nbtor_refined 0.214 r_symmetry_nbd_other 0.213 r_nbd_refined 0.205 r_nbd_other 0.164 r_xyhbond_nbd_refined 0.149 r_symmetry_nbd_refined 0.134 r_symmetry_xyhbond_nbd_other 0.111 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.055 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 42
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing