5E5F

X-ray structure of the complex between RNase A and compound 4-PF6 ([(PPh3)Au(mi-pbi)Pt(Me)(DMSO)][PF6]), the heterobimetallic derivative obtained in the reaction between the organometallic compound [Pt(pbi)(Me)(DMSO)], pbi=2-(2'-pyridil)benzimidazole (compound 3) and the gold(I) compound [Au(Ph3P)][PF6]


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP298RNase A crystals were obtained using the procedure previously described by Vitagliano et al., 200028. Briefly, crystals of the protein were grown by hanging drop vapor diffusion method using a reservoir solution containing 22-24 % (w/v) PEG4K, 10 mM sodium citrate pH 5.1-5.3. The crystals are monoclinic, space group C2, with two molecules in the asymmetric unit. The adducts were prepared by a three-days soaking in a solution that comprised the standard mother liquor used for the crystal growth to which a 2.5-5 mM solution of each compound was added. Crystal soaked in this solution were mounted for the X-ray data collection without using a cryoprotectant, as done in previous studies30.
Crystal Properties
Matthews coefficientSolvent content
1.9537.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.487α = 90
b = 31.215β = 90.69
c = 69.012γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2015-03-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6869956.52.423228
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.681.7188.50.29421.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT1.686922040118894.710.186010.183320.23404RANDOM30.167
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]
-0.01-0.170.33-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.93
r_dihedral_angle_4_deg13.81
r_dihedral_angle_3_deg13.134
r_dihedral_angle_1_deg6.848
r_long_range_B_other6.562
r_long_range_B_refined6.544
r_scangle_other4.784
r_mcangle_it3.354
r_mcangle_other3.353
r_scbond_it3.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.93
r_dihedral_angle_4_deg13.81
r_dihedral_angle_3_deg13.134
r_dihedral_angle_1_deg6.848
r_long_range_B_other6.562
r_long_range_B_refined6.544
r_scangle_other4.784
r_mcangle_it3.354
r_mcangle_other3.353
r_scbond_it3.28
r_scbond_other3.279
r_mcbond_it2.526
r_mcbond_other2.515
r_angle_refined_deg1.873
r_angle_other_deg0.883
r_chiral_restr0.104
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1898
Nucleic Acid Atoms
Solvent Atoms186
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing