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X-ray structure of the adduct between bovine pancreatic ribonuclease and Auoxo6, a dinuclear gold(III) complex with -dioxo bridges linking the two metal centers
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4L55 PDB entry 4L55
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 20% PEG4000 and 20 mM sodium citrate buffer pH 5.0. Crystals appeared within 7 days. After two weeks, crystals were soaked in a solution of the gold-based drug dissolved in DMSO and in 50 mM sodium citrate buffer pH 5.0. At the final, concentrations of metallodrugs and protein were in at least 1:1 ratio., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.96 37.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.595 α = 90 b = 31.297 β = 90.53 c = 69.027 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN 944 2013-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.25 23 94.7 9860 9860
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.27 94.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 4L55 2.25 23 9349 9349 471 93.67 0.18937 0.18937 0.18542 0.1912 0.26848 0.2746 RANDOM 35.251
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.195 r_dihedral_angle_3_deg 15.641 r_dihedral_angle_4_deg 14.272 r_dihedral_angle_1_deg 6.571 r_angle_refined_deg 1.489 r_angle_other_deg 0.753 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.195 r_dihedral_angle_3_deg 15.641 r_dihedral_angle_4_deg 14.272 r_dihedral_angle_1_deg 6.571 r_angle_refined_deg 1.489 r_angle_other_deg 0.753 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1902 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement