7BD7

X-ray structure of Arsenoplatin-1-encapsulated horse spleen ferritin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5ERK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.22930.6 M ammomium sulphate 0.1 M Tris HCl buffer pH 7.2 60 mM cadmium sulphate
Crystal Properties
Matthews coefficientSolvent content
3.160.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 180.91α = 90
b = 180.91β = 90
c = 180.91γ = 90
Symmetry
Space GroupF 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 4M2019-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-30.9677ESRFMASSIF-3

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
11.541.5381000.1130.120.040.99912.48.740897
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)
11.51.531000.840.8910.4040.5632.69.1

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 REPLACEMENTTHROUGHOUT5erk1.541.5438816205999.870.16730.16630.1851RANDOM17.101
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.904
r_dihedral_angle_4_deg19.485
r_dihedral_angle_3_deg14.283
r_dihedral_angle_1_deg5.701
r_angle_refined_deg1.819
r_angle_other_deg1.631
r_chiral_restr0.098
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.904
r_dihedral_angle_4_deg19.485
r_dihedral_angle_3_deg14.283
r_dihedral_angle_1_deg5.701
r_angle_refined_deg1.819
r_angle_other_deg1.631
r_chiral_restr0.098
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1379
Nucleic Acid Atoms
Solvent Atoms210
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
STARANISOdata scaling
PHASERphasing