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De novo photoenzyme photoABLE1 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 35 % (w/v) PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.04 39.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.34 α = 90 b = 46.89 β = 90 c = 54.09 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 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 1.15 30 99 0.086 11.67 6.3 41272
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 1.15 1.25 98.2 0.237 5.44 6.5
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 1.15 30 39207 2063 99.02 0.15067 0.14927 0.157 0.17716 0.1832 RANDOM 12.764
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] -0.88 0.44 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.216 r_dihedral_angle_4_deg 18.7 r_dihedral_angle_3_deg 11.935 r_dihedral_angle_1_deg 2.893 r_long_range_B_refined 2.745 r_long_range_B_other 2.192 r_scangle_other 1.866 r_angle_other_deg 1.751 r_angle_refined_deg 1.548 r_scbond_it 1.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.216 r_dihedral_angle_4_deg 18.7 r_dihedral_angle_3_deg 11.935 r_dihedral_angle_1_deg 2.893 r_long_range_B_refined 2.745 r_long_range_B_other 2.192 r_scangle_other 1.866 r_angle_other_deg 1.751 r_angle_refined_deg 1.548 r_scbond_it 1.513 r_scbond_other 1.512 r_rigid_bond_restr 1.254 r_mcangle_it 1.124 r_mcangle_other 1.124 r_mcbond_other 0.809 r_mcbond_it 0.808 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 986 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing