6GOK

X-ray structure of the adduct formed upon reaction of bovine pancreatic ribonuclease with a Pd(II) complex bearing N,N-pyridylbenzimidazole derivative with an alkylated sulphonate side chain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FS3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.129320% PEG4000 10 mM sodium citrate buffer pH 5.1
Crystal Properties
Matthews coefficientSolvent content
2.1843.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.282α = 90
b = 32.805β = 90.61
c = 72.661γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442018-03-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.6572.6691.10.0912.12.56649
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.652.779.20.3910.8341.62.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1fs32.6572.66619630991.220.190660.187220.25476RANDOM48.959
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]
-1.21.351.43-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.104
r_dihedral_angle_3_deg16.515
r_dihedral_angle_4_deg12.549
r_long_range_B_refined8.045
r_long_range_B_other8.043
r_dihedral_angle_1_deg7.087
r_mcangle_it5.287
r_mcangle_other5.286
r_scangle_other5.062
r_mcbond_it3.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.104
r_dihedral_angle_3_deg16.515
r_dihedral_angle_4_deg12.549
r_long_range_B_refined8.045
r_long_range_B_other8.043
r_dihedral_angle_1_deg7.087
r_mcangle_it5.287
r_mcangle_other5.286
r_scangle_other5.062
r_mcbond_it3.301
r_mcbond_other3.301
r_scbond_it3.087
r_scbond_other3.086
r_angle_refined_deg1.637
r_angle_other_deg1.205
r_chiral_restr0.079
r_gen_planes_refined0.013
r_bond_refined_d0.012
r_gen_planes_other0.007
r_bond_other_d0.005
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 Atoms1902
Nucleic Acid Atoms
Solvent Atoms63
Heterogen Atoms49

Software

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