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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)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ERK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 298 0.6 M ammonium sulfate
0.1 M Tris HCl pH 7.4
60 mM cadmium sulfate
Crystal Properties Matthews coefficient Solvent content 3.1 60.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.832 α = 90 b = 180.832 β = 90 c = 180.832 γ = 90
Symmetry Space Group F 4 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN 944 2016-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.8 104.4 99.8 0.104 0.052 18.4 8.7 24060
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) Redundancy Number Unique Reflections (All) 1 1.8 1.83 98 0.717 0.402 2 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5ERK 1.8 104.4 22820 1187 99.78 0.16542 0.16379 0.1758 0.19745 0.2071 RANDOM 17.878
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.178 r_dihedral_angle_4_deg 21.531 r_dihedral_angle_3_deg 13.492 r_long_range_B_refined 7.126 r_long_range_B_other 6.695 r_dihedral_angle_1_deg 6.306 r_scangle_other 5.204 r_scbond_it 4.14 r_scbond_other 3.937 r_mcangle_it 3.401
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.178 r_dihedral_angle_4_deg 21.531 r_dihedral_angle_3_deg 13.492 r_long_range_B_refined 7.126 r_long_range_B_other 6.695 r_dihedral_angle_1_deg 6.306 r_scangle_other 5.204 r_scbond_it 4.14 r_scbond_other 3.937 r_mcangle_it 3.401 r_mcangle_other 3.399 r_mcbond_it 2.181 r_mcbond_other 2.137 r_angle_refined_deg 2.076 r_angle_other_deg 1.135 r_chiral_restr 0.13 r_bond_refined_d 0.044 r_gen_planes_refined 0.011 r_bond_other_d 0.006 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 1379 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing