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De novo photoenzyme variant ABLE-E116C-TXT V111H-L53A (photoABLE2 precursor) in complex with substrate
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 M Ammonium fluoride
20 % (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.86 33.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.51 α = 90 b = 46.57 β = 90 c = 47.29 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 X 16M 2025-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9763 PETRA III, EMBL c/o DESY P14 (MX2)
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 96.4 0.061 17.42 5.1 20104
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 95.8 0.061 4.42 5.21
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 27.01 19098 1006 96.43 0.18833 0.18633 0.1939 0.22599 0.225 RANDOM 15.867
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] -0.66 -1.52 2.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.036 r_dihedral_angle_4_deg 17.291 r_dihedral_angle_3_deg 12.771 r_dihedral_angle_1_deg 3.165 r_long_range_B_refined 2.654 r_long_range_B_other 2.217 r_scangle_other 1.481 r_angle_other_deg 1.421 r_mcangle_other 1.298 r_mcangle_it 1.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.036 r_dihedral_angle_4_deg 17.291 r_dihedral_angle_3_deg 12.771 r_dihedral_angle_1_deg 3.165 r_long_range_B_refined 2.654 r_long_range_B_other 2.217 r_scangle_other 1.481 r_angle_other_deg 1.421 r_mcangle_other 1.298 r_mcangle_it 1.294 r_scbond_it 1.235 r_scbond_other 1.234 r_angle_refined_deg 1.12 r_mcbond_it 1.008 r_mcbond_other 0.997 r_rigid_bond_restr 0.972 r_chiral_restr 0.054 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 923 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing