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Crystal structure of designed two-component self-assembling icosahedral cage I53-40
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B98 Rosetta design generated based on the PDB files 2b98 and 4e38, but with differences experimental model PDB 4E38 Rosetta design generated based on the PDB files 2b98 and 4e38, but with differences
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 100 mM sodium acetate pH 4.6, 0.4 M calcium chloride, 3.2% (v/v) isoproponal
Crystal Properties Matthews coefficient Solvent content 4.64 73.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 265.62 α = 90 b = 279.81 β = 90 c = 301.33 γ = 90
Symmetry Space Group I 2 2 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 PILATUS 6M-F 2014-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979100 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.699 199.3 99 0.168 0.992 8.34 4.2 118064 -3 70.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.7 3.8 95.1 0.844 1.84
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE Rosetta design generated based on the PDB files 2b98 and 4e38, but with differences 3.699 199.257 1.35 118004 11798 98.92 0.2407 0.24 0.2404 0.2468 0.2473 99.5539
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 f_dihedral_angle_d 14.436 f_angle_d 1.347 f_chiral_restr 0.084 f_bond_d 0.011 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 39198 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction XDS data reduction