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De novo photoenzyme variant ABLE-E116C-TXT H49A-L42T (photoABLE1 precursor) in complex with substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AlphaFold3 apo structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M Tris/HCl pH 8.5
25 % (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.26 45.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.79 α = 94.48 b = 40 β = 97.94 c = 87.41 γ = 110.75
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 EIGER X 16M 2025-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.4 30 93.3 0.069 7.47 3.45 90893
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 1.4 1.5 94.4 0.624 1.66 3.62
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.4 30 86343 4544 93.28 0.26184 0.25999 0.2665 0.29611 0.2841 RANDOM 22.184
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] -0.29 0.39 0.61 -0.8 0.1 0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.616 r_dihedral_angle_4_deg 21.338 r_dihedral_angle_3_deg 13.824 r_long_range_B_refined 3.533 r_dihedral_angle_1_deg 3.334 r_long_range_B_other 3.331 r_scangle_other 3.072 r_scbond_it 2.626 r_scbond_other 2.625 r_mcangle_it 2.334
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.616 r_dihedral_angle_4_deg 21.338 r_dihedral_angle_3_deg 13.824 r_long_range_B_refined 3.533 r_dihedral_angle_1_deg 3.334 r_long_range_B_other 3.331 r_scangle_other 3.072 r_scbond_it 2.626 r_scbond_other 2.625 r_mcangle_it 2.334 r_mcangle_other 2.334 r_mcbond_it 1.947 r_mcbond_other 1.945 r_angle_other_deg 1.4 r_angle_refined_deg 1.362 r_rigid_bond_restr 1.356 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3927 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing