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De novo photoenzyme photoABLE1
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 6.5 293 0.1 M MES pH 6.5
25 % (w/v) PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.06 40.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.93 α = 90 b = 45.59 β = 92.52 c = 54.51 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 1.15 30 98.1 0.063 10.09 3.3 80196
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 97.6 0.331 3.24 3.4
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 76185 4010 98.13 0.1758 0.174 0.1812 0.20951 0.21 RANDOM 15.076
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] 0.52 -0.43 -0.46 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.115 r_dihedral_angle_4_deg 18.631 r_dihedral_angle_3_deg 12.957 r_rigid_bond_restr 3.36 r_long_range_B_refined 3.109 r_dihedral_angle_1_deg 3.061 r_long_range_B_other 2.639 r_scangle_other 2.29 r_scbond_it 2.016 r_scbond_other 2.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.115 r_dihedral_angle_4_deg 18.631 r_dihedral_angle_3_deg 12.957 r_rigid_bond_restr 3.36 r_long_range_B_refined 3.109 r_dihedral_angle_1_deg 3.061 r_long_range_B_other 2.639 r_scangle_other 2.29 r_scbond_it 2.016 r_scbond_other 2.015 r_angle_refined_deg 1.759 r_mcangle_it 1.449 r_mcangle_other 1.449 r_mcbond_it 1.164 r_mcbond_other 1.163 r_angle_other_deg 0.775 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d 0.004 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 1972 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing