☰ Navigation Tabs
RAPTA-C (Ruthenium[II]-cymene-phosphaadamantane) cancer drug binding to the nucleosome core
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NZD
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 2.69 54.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.35 α = 90 b = 109.86 β = 90 c = 182.59 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 PSI PILATUS 6M 2009-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.5 SLS X06SA
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 2.3 94.1 96.5 0.994 8.6 4.8 92229
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 2.3 2.42 0.576
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 2.3 94.1 92082 1846 96.36 0.228 0.2272 0.2288 0.2556 0.2586 91.737
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] 1.577 -3.64 2.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.9 r_dihedral_angle_6_deg 14.853 r_lrange_it 12.641 r_lrange_other 12.641 r_scangle_it 9.264 r_scangle_other 9.264 r_mcangle_it 6.358 r_mcangle_other 6.357 r_scbond_it 6.147 r_scbond_other 6.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.9 r_dihedral_angle_6_deg 14.853 r_lrange_it 12.641 r_lrange_other 12.641 r_scangle_it 9.264 r_scangle_other 9.264 r_mcangle_it 6.358 r_mcangle_other 6.357 r_scbond_it 6.147 r_scbond_other 6.146 r_dihedral_angle_2_deg 5.932 r_dihedral_angle_1_deg 5.518 r_mcbond_it 4.328 r_mcbond_other 4.327 r_angle_refined_deg 1.412 r_dihedral_angle_other_2_deg 0.691 r_angle_other_deg 0.434 r_nbtor_refined 0.211 r_symmetry_nbd_other 0.204 r_metal_ion_refined 0.202 r_nbd_refined 0.197 r_nbd_other 0.157 r_xyhbond_nbd_refined 0.148 r_symmetry_nbd_refined 0.137 r_symmetry_xyhbond_nbd_refined 0.135 r_symmetry_nbtor_other 0.076 r_symmetry_xyhbond_nbd_other 0.069 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 22 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing