7PNI

X-ray structure of the adduct formed upon reaction of Pt(II) complex 2c with ribonuclease A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.129322% PEG4K 10 mM sodium citrate pH 5.1
Crystal Properties
Matthews coefficientSolvent content
2.1442.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.14α = 90
b = 31.79β = 90.347
c = 73.74γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C0.96ELETTRA11.2C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.1328.04990.0780.0860.0340.99814.56.213153
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.132.1797.30.6430.7210.3180.8982.34.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1jvt2.1328.041312867498.1830.1970.19230.27539.806
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]
-0.143-0.192-0.0720.217
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.316
r_dihedral_angle_3_deg15.553
r_dihedral_angle_4_deg15.093
r_lrange_it9.283
r_lrange_other9.28
r_dihedral_angle_1_deg7.775
r_scangle_it6.656
r_scangle_other6.465
r_mcangle_it6.109
r_mcangle_other6.105
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.316
r_dihedral_angle_3_deg15.553
r_dihedral_angle_4_deg15.093
r_lrange_it9.283
r_lrange_other9.28
r_dihedral_angle_1_deg7.775
r_scangle_it6.656
r_scangle_other6.465
r_mcangle_it6.109
r_mcangle_other6.105
r_scbond_it4.178
r_scbond_other4.174
r_mcbond_other3.913
r_mcbond_it3.912
r_angle_refined_deg2.195
r_angle_other_deg1.322
r_nbd_other0.223
r_nbd_refined0.206
r_xyhbond_nbd_refined0.204
r_symmetry_nbd_refined0.198
r_symmetry_nbd_other0.187
r_symmetry_xyhbond_nbd_refined0.168
r_nbtor_refined0.16
r_symmetry_xyhbond_nbd_other0.136
r_symmetry_nbtor_other0.085
r_chiral_restr0.073
r_xyhbond_nbd_other0.028
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_ext_dist_refined_d0.004
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1885
Nucleic Acid Atoms
Solvent Atoms139
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
autoPROCdata scaling
PHASERphasing