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Crystal structure of designed two-component self-assembling icosahedral cage I52-32
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JFB Rosetta design generated based on the PDB files 2jfb and 3lfh, but with differences experimental model PDB 3LFH Rosetta design generated based on the PDB files 2jfb and 3lfh, but with differences
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 0.17 M potassium sodium tartrate tetrahydrate
Crystal Properties Matthews coefficient Solvent content 6.22 80.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 258.82 α = 90 b = 258.82 β = 90 c = 641.73 γ = 120
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 2015-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97920 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 3.5 213.9 99.1 0.132 0.991 7.31 3.6 200420 -3 104.79
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 3.5 3.59 97.5 0.674 1.9
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 2jfb and 3lfh, but with differences 3.5 110.724 1.93 200301 20026 99.05 0.2275 0.2269 0.2287 0.2334 0.2347 103.0777
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 13.237 f_angle_d 1.071 f_chiral_restr 0.068 f_bond_d 0.008 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 40538 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