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De novo design of protein catalysts for new-to-nature reactions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other ESMfold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1M Tris HCl pH 8.5 and 2.0M Ammonium phosphate monobasic
Crystal Properties Matthews coefficient Solvent content 2.4 48.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.273 α = 90 b = 71.273 β = 90 c = 114.942 γ = 90
Symmetry Space Group I 41 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 PIXEL DECTRIS PILATUS3 6M 2024-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim 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 2.255 60.57 99.78 0.148 0.996 7 2 7287 39.65
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 2.255 2.33 0.311
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 2.26 60.57 1.34 7287 729 99.78 0.2364 0.2316 0.2311 0.2783 0.2773 49.89
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 24.3109 f_angle_d 1.3812 f_chiral_restr 0.0427 f_plane_restr 0.0206 f_bond_d 0.0193
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 901 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing