6FX8

The X-ray structure of the ferritin nanocage containing Au and Pt, obtained upon encapsulation of a single heterobimetallic compound within the protein cage (rotating anode data)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42980.6 M ammonium sulfate 0.1 M Tris HCl pH 7.4 60 mM cadmium sulfate
Crystal Properties
Matthews coefficientSolvent content
3.160.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 180.832α = 90
b = 180.832β = 90
c = 180.832γ = 90
Symmetry
Space GroupF 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442016-06-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.8104.499.80.1040.05218.48.724060
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.83980.7170.40224.6

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 REPLACEMENTTHROUGHOUT5ERK1.8104.422820118799.780.165420.163790.19745RANDOM17.878
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_deg37.178
r_dihedral_angle_4_deg21.531
r_dihedral_angle_3_deg13.492
r_long_range_B_refined7.126
r_long_range_B_other6.695
r_dihedral_angle_1_deg6.306
r_scangle_other5.204
r_scbond_it4.14
r_scbond_other3.937
r_mcangle_it3.401
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.178
r_dihedral_angle_4_deg21.531
r_dihedral_angle_3_deg13.492
r_long_range_B_refined7.126
r_long_range_B_other6.695
r_dihedral_angle_1_deg6.306
r_scangle_other5.204
r_scbond_it4.14
r_scbond_other3.937
r_mcangle_it3.401
r_mcangle_other3.399
r_mcbond_it2.181
r_mcbond_other2.137
r_angle_refined_deg2.076
r_angle_other_deg1.135
r_chiral_restr0.13
r_bond_refined_d0.044
r_gen_planes_refined0.011
r_bond_other_d0.006
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1379
Nucleic Acid Atoms
Solvent Atoms259
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing