8RI3

Crystal structure of transplatin/B-DNA adduct obtained upon 7 days 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
2.3146.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 25.56α = 90
b = 40.39β = 90
c = 65.67γ = 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
11.434.40498.90.99813.29.713972
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)
11.41.421000.6010.99.5

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-VALUE1.434.4041233059188.1410.2180.21590.256715.483
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]
0.058-0.1490.091
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it5.531
r_lrange_other5.412
r_scangle_it3.712
r_scangle_other3.708
r_angle_refined_deg3.046
r_scbond_it2.405
r_scbond_other1.977
r_angle_other_deg0.494
r_nbd_refined0.249
r_nbtor_refined0.245
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it5.531
r_lrange_other5.412
r_scangle_it3.712
r_scangle_other3.708
r_angle_refined_deg3.046
r_scbond_it2.405
r_scbond_other1.977
r_angle_other_deg0.494
r_nbd_refined0.249
r_nbtor_refined0.245
r_symmetry_nbd_other0.214
r_xyhbond_nbd_refined0.17
r_nbd_other0.155
r_chiral_restr0.149
r_symmetry_xyhbond_nbd_refined0.115
r_symmetry_nbtor_other0.096
r_metal_ion_refined0.095
r_symmetry_nbd_refined0.049
r_gen_planes_refined0.03
r_bond_refined_d0.009
r_bond_other_d0.002
r_gen_planes_other0.001
r_ext_dist_refined_b
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms486
Solvent Atoms109
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing