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Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BRO PDB entries 1BRO, 1AA7 experimental model PDB 1AA7 PDB entries 1BRO, 1AA7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10.3 298 1.2M NaH2PO4, 0.8M K2HPO4, 0.1M CAPS, pH 10.3, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.65 53.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.59 α = 90 b = 127.71 β = 90 c = 204.22 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 IMAGE PLATE RIGAKU RAXIS HTC 2011-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 19.73 68.3 0.206 7.9 4.95 22135 -3 38.558
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 3.08 20.4 0.669 2.91
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 THROUGHOUT PDB entries 1BRO, 1AA7 3.002 19.728 1.99 22131 1133 68.63 0.2312 0.2285 0.2246 0.2813 0.2819 54.1428
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] -7.6483 -7.6447 -5.1296
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.692 f_angle_d 0.555 f_chiral_restr 0.04 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10149 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction HKL-3000 data collection XDS data reduction