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RAPTA-6MB (Ruthenium[II]-hexamethylbenzene-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 2.71 54.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.11 α = 90 b = 110.03 β = 90 c = 182.33 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 2.99 76.7 99.3 0.997 11.3 5.4 44021
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 2.99 3.15 0.558
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 2.99 70.838 43956 912 99.212 0.219 0.2184 0.2193 0.2675 0.217 121.276
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] 1.351 -5.523 4.172
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 19.329 r_lrange_it 19.328 r_dihedral_angle_3_deg 16.214 r_dihedral_angle_6_deg 15.712 r_scangle_it 15.23 r_scangle_other 15.229 r_mcangle_it 9.944 r_mcangle_other 9.943 r_scbond_it 9.775 r_scbond_other 9.775
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 19.329 r_lrange_it 19.328 r_dihedral_angle_3_deg 16.214 r_dihedral_angle_6_deg 15.712 r_scangle_it 15.23 r_scangle_other 15.229 r_mcangle_it 9.944 r_mcangle_other 9.943 r_scbond_it 9.775 r_scbond_other 9.775 r_mcbond_it 6.678 r_mcbond_other 6.673 r_dihedral_angle_1_deg 5.814 r_dihedral_angle_2_deg 5.538 r_angle_refined_deg 1.462 r_dihedral_angle_other_2_deg 0.865 r_angle_other_deg 0.439 r_nbtor_refined 0.216 r_symmetry_nbd_other 0.21 r_nbd_refined 0.205 r_symmetry_nbd_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.171 r_xyhbond_nbd_refined 0.164 r_nbd_other 0.147 r_symmetry_xyhbond_nbd_other 0.124 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.056 r_gen_planes_refined 0.005 r_bond_refined_d 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 39
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing