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De novo designed alpha helical toroidal protein with a Ru-cofactor
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 293 0.1 M Na Acet 5 pH, 2 M Na Form
Crystal Properties Matthews coefficient Solvent content 2.23 44.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.276 α = 90 b = 91.276 β = 90 c = 123.948 γ = 90
Symmetry Space Group I 41 2 2
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 2024-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.9 73.5 93.8 0.147 0.15 0.029 1 15.06 25.7 5750
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.004 99 4.436 4.525 0.887 0.543 0.63 25.7
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 FREE R-VALUE 2.9 73.5 5434 312 94.24 0.22084 0.21795 0.2447 0.26848 0.2936 RANDOM 122.841
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] -0.15 -0.15 0.29
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 20.018 r_long_range_B_other 20.013 r_scangle_other 16.881 r_dihedral_angle_3_deg 16.172 r_mcangle_other 13.581 r_mcangle_it 13.579 r_scbond_it 10.787 r_scbond_other 10.782 r_mcbond_it 9.253 r_mcbond_other 9.246
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 20.018 r_long_range_B_other 20.013 r_scangle_other 16.881 r_dihedral_angle_3_deg 16.172 r_mcangle_other 13.581 r_mcangle_it 13.579 r_scbond_it 10.787 r_scbond_other 10.782 r_mcbond_it 9.253 r_mcbond_other 9.246 r_dihedral_angle_2_deg 6.55 r_dihedral_angle_1_deg 4.894 r_angle_refined_deg 1.811 r_angle_other_deg 0.513 r_chiral_restr 0.15 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1561 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing