5NJ7

The X-ray structure of the adduct formed in the reaction between bovine pancreatic ribonuclease and arsenoplatin-1


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.129822% w/v PEG4K, 10 mM sodium acetate pH 5.1. Crystals of RNase A-AP-1 were formed by soaking pre-grown RNase A crystals for 3 h in a solution containing 5 mM AP-1 dissolved in DMSO and then added to the reservoir.
Crystal Properties
Matthews coefficientSolvent content
2.244.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.535α = 90
b = 32.855β = 90.17
c = 72.939γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944mirrors2014-10-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
12.1572.9499.70.117103.413274

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 REPLACEMENTTHROUGHOUT1JVT2.1572.941252668199.50.19040.187040.25049RANDOM33.698
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]
-1.33-0.190.161.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.616
r_dihedral_angle_3_deg14.759
r_dihedral_angle_4_deg13.999
r_dihedral_angle_1_deg7.077
r_long_range_B_refined7.023
r_long_range_B_other6.784
r_scangle_other4.444
r_mcangle_other4.155
r_mcangle_it4.154
r_scbond_it3.148
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.616
r_dihedral_angle_3_deg14.759
r_dihedral_angle_4_deg13.999
r_dihedral_angle_1_deg7.077
r_long_range_B_refined7.023
r_long_range_B_other6.784
r_scangle_other4.444
r_mcangle_other4.155
r_mcangle_it4.154
r_scbond_it3.148
r_scbond_other2.745
r_mcbond_it2.65
r_mcbond_other2.647
r_angle_refined_deg1.709
r_angle_other_deg0.802
r_chiral_restr0.09
r_bond_refined_d0.014
r_gen_planes_refined0.008
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 Atoms1902
Nucleic Acid Atoms
Solvent Atoms142
Heterogen Atoms48

Software

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