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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 (synchrtron 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 3.14 60.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.68 α = 90 b = 181.68 β = 90 c = 181.68 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 PIXEL DECTRIS PILATUS3 2M 2016-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9677 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.5 104.9 99.8 0.1 0.039 0.998 12.4 8.3 41265
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.58 99.6 0.744 0.279 0.592 2.9 8.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5ERK 1.5 104.89 39257 2004 99.62 0.15348 0.15194 0.18282 0.1741 RANDOM 18.241
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 36.905 r_dihedral_angle_4_deg 22.173 r_dihedral_angle_3_deg 12.717 r_long_range_B_refined 7.527 r_long_range_B_other 7.043 r_scangle_other 5.699 r_dihedral_angle_1_deg 5.459 r_scbond_it 3.997 r_scbond_other 3.995 r_mcangle_it 2.833
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.905 r_dihedral_angle_4_deg 22.173 r_dihedral_angle_3_deg 12.717 r_long_range_B_refined 7.527 r_long_range_B_other 7.043 r_scangle_other 5.699 r_dihedral_angle_1_deg 5.459 r_scbond_it 3.997 r_scbond_other 3.995 r_mcangle_it 2.833 r_mcangle_other 2.833 r_angle_refined_deg 2.199 r_mcbond_it 1.956 r_mcbond_other 1.903 r_angle_other_deg 1.088 r_chiral_restr 0.136 r_bond_refined_d 0.03 r_gen_planes_refined 0.012 r_bond_other_d 0.002 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 230 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing