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Crystal structure of an AI-designed TIM-barrel F15C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other Designed model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 30% PEG3350, 0.150M Magnesium acetate tetrahydrate, 0.1 M Bis Tris (pH 6.0)
Crystal Properties Matthews coefficient Solvent content 2.27 45.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.23 α = 90 b = 103.57 β = 90.39 c = 80.94 γ = 90
Symmetry Space Group P 1 21 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 2021-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.9 38.93 99.2 0.142 0.147 0.997 10 13.908 56979 43.146
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 99.8 1.546 1.604 0.743 1.49 14.146
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Designed model 1.9 38.93 54130 2849 99.24 0.1809 0.1768 0.2568 0.2828 RANDOM 49.773
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] 5.42 0.53 -2.56 -2.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.012 r_dihedral_angle_3_deg 16.856 r_rigid_bond_restr 10.871 r_dihedral_angle_4_deg 10.676 r_dihedral_angle_1_deg 6.206 r_angle_refined_deg 1.353 r_angle_other_deg 1.256 r_chiral_restr 0.055 r_bond_other_d 0.009 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.012 r_dihedral_angle_3_deg 16.856 r_rigid_bond_restr 10.871 r_dihedral_angle_4_deg 10.676 r_dihedral_angle_1_deg 6.206 r_angle_refined_deg 1.353 r_angle_other_deg 1.256 r_chiral_restr 0.055 r_bond_other_d 0.009 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5684 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction PHASER phasing