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De novo design cavitated protein without predefined topology
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold alphafold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 289 20% PEG3350, 0.2 M di-Ammonium hydrogen Citrate
Crystal Properties Matthews coefficient Solvent content 2.47 50.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.547 α = 90 b = 72.593 β = 115.797 c = 103.518 γ = 90
Symmetry Space Group C 1 2 1
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 2021-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979150 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.71 50 96.12 0.997 11.34 3.5 29506 53.86
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.71 2.807 0.642
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE alphafold 2.71 41.86 1.33 29480 2730 91.18 0.2381 0.2367 0.2662 0.2431 72.71
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 14.0612 f_angle_d 0.7395 f_chiral_restr 0.0404 f_plane_restr 0.0053 f_bond_d 0.0043
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6278 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction PHASER phasing Aimless data scaling PHENIX model building