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Crystal structure of T33-27.1: Deep-learning sequence design of co-assembling tetrahedron protein nanoparticles
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other De novo Designed model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.12 M ethylene glycol, 0.1 M Tris-Bicine, pH 8.5, 30% v/v glycerol + PEG4000
Crystal Properties Matthews coefficient Solvent content 2.8 56.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 176.515 α = 90 b = 176.515 β = 90 c = 176.515 γ = 90
Symmetry Space Group P 21 3
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 ADSC QUANTUM 315r 2021-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 0.99994 ALS 8.2.1
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 3.63 100 100 0.229 0.998 22.69 21.5 20978 69.85
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.63 3.72 100 0.063 0.961 21.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.63 48.96 1.33 20763 1999 98.97 0.2186 0.2142 0.2147 0.2585 0.259 91.68
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 10.721 f_angle_d 0.4321 f_chiral_restr 0.0428 f_plane_restr 0.0039 f_bond_d 0.0016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11075 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-3000 data reduction SCALEPACK data scaling PHASER phasing