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De novo photoenzyme variant ABLE-E116C-TXT H49A-L42T (photoABLE1 precursor) in complex with product formed in crystallo after irradiation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2 Potassium fluoride
20 % (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.15 42.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.68 α = 90 b = 82.09 β = 110.2 c = 39.69 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 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 1.5 30 97.4 0.055 11.98 3.52 37382
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 1.5 1.6 96.4 0.65 1.88 3.43
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 1.5 30 35416 1864 97.6 0.17719 0.1752 0.1655 0.21433 0.1844 RANDOM 24.416
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] 0.49 0.21 -1.39 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.362 r_dihedral_angle_4_deg 16.711 r_dihedral_angle_3_deg 14.311 r_long_range_B_refined 3.898 r_long_range_B_other 3.743 r_scangle_other 3.418 r_scbond_it 2.805 r_scbond_other 2.804 r_dihedral_angle_1_deg 2.773 r_mcangle_other 2.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.362 r_dihedral_angle_4_deg 16.711 r_dihedral_angle_3_deg 14.311 r_long_range_B_refined 3.898 r_long_range_B_other 3.743 r_scangle_other 3.418 r_scbond_it 2.805 r_scbond_other 2.804 r_dihedral_angle_1_deg 2.773 r_mcangle_other 2.22 r_mcangle_it 2.218 r_mcbond_it 1.771 r_mcbond_other 1.766 r_angle_other_deg 1.49 r_angle_refined_deg 1.355 r_rigid_bond_restr 1.271 r_chiral_restr 0.062 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.003 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 1968 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing