8OO3

X-ray structure of the adduct formed upon reaction of cisplatin with human angiogenin after 5 days soaking


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.129310% PEG6K, 20 mM sodium citrate pH 5.1, 0.2 M sodium/potassium tartrate
Crystal Properties
Matthews coefficientSolvent content
2.1643.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.32α = 90
b = 37.48β = 90
c = 38.33γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C1.00ELETTRA11.2C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.7642.66950.083119.110.712229
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)
11.761.7983.20.6360.8562.36.4

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 REPLACEMENTTHROUGHOUT1.7642.661211461994.8930.2450.2430.290520.824
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]
-0.149-0.0490.198
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.606
r_dihedral_angle_4_deg17.403
r_dihedral_angle_3_deg16.088
r_dihedral_angle_1_deg8.04
r_lrange_it6.535
r_lrange_other6.52
r_scangle_it4.093
r_scangle_other4.092
r_mcangle_other3.464
r_mcangle_it3.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.606
r_dihedral_angle_4_deg17.403
r_dihedral_angle_3_deg16.088
r_dihedral_angle_1_deg8.04
r_lrange_it6.535
r_lrange_other6.52
r_scangle_it4.093
r_scangle_other4.092
r_mcangle_other3.464
r_mcangle_it3.46
r_scbond_it2.577
r_scbond_other2.561
r_mcbond_it2.177
r_mcbond_other2.151
r_angle_refined_deg1.724
r_angle_other_deg1.353
r_symmetry_xyhbond_nbd_refined0.259
r_nbd_other0.232
r_nbd_refined0.191
r_symmetry_nbd_other0.187
r_symmetry_nbd_refined0.164
r_nbtor_refined0.159
r_xyhbond_nbd_refined0.133
r_chiral_restr0.082
r_symmetry_nbtor_other0.079
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms985
Nucleic Acid Atoms
Solvent Atoms94
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing