8RI5

Crystal structure of transplatin/B-DNA adduct obtained upon 48 h of soaking


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3U2N 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52937-14% (v/v) 2-methyl-2,4-pentanediol (MPD), 20 mM MgCl2, 80 mM spermine tetrahydrochloride, and 60 mM sodium cacodylate pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.346.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 25.474α = 90
b = 40.221β = 90
c = 65.676γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2023-10-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C1.00ELETTRA11.2C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.4125.4789.90.99930.51012070
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.411.4551.90.8322.54.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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-VALUE1.41525.451204560189.4740.1920.18970.229517.203
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]
0.7650.262-1.027
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it4.723
r_lrange_other4.219
r_angle_refined_deg3.199
r_scangle_it3.005
r_scangle_other3.003
r_scbond_it2.045
r_scbond_other2.045
r_angle_other_deg0.484
r_nbtor_refined0.252
r_symmetry_nbd_other0.213
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it4.723
r_lrange_other4.219
r_angle_refined_deg3.199
r_scangle_it3.005
r_scangle_other3.003
r_scbond_it2.045
r_scbond_other2.045
r_angle_other_deg0.484
r_nbtor_refined0.252
r_symmetry_nbd_other0.213
r_chiral_restr0.162
r_nbd_refined0.151
r_symmetry_xyhbond_nbd_refined0.147
r_xyhbond_nbd_refined0.144
r_nbd_other0.144
r_symmetry_nbtor_other0.092
r_symmetry_nbd_refined0.065
r_gen_planes_refined0.036
r_bond_refined_d0.011
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms486
Solvent Atoms121
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing