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Crystal structure of a computationally designed protein bound to a Ru-containing cofactor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Unpublished structure of apo protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Crystal 1: 24% PEG 3350, 2% PEG 400, 50 mM HEPES pH 6.8, 150 mM NaCl
Crystal 2: 22% PEG 8000, 100 mM Na cacodylate, 200 mM Na acetate trihydrate pH 5
Crystal Properties Matthews coefficient Solvent content 2.26 45.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.165 α = 90 b = 85.142 β = 90 c = 90.235 γ = 90
Symmetry Space Group I 2 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 2023-11-26 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) 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 45.81 100 0.026 1 10.79 26.6 4786
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.08 100 0.797 0.807 1.3 25.5
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.9 45.1 4786 99.64 0.2631 0.2554 0.3184 0.2966 RANDOM 143.3
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] -8.59 -2.83 11.42
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 27.481 r_long_range_B_other 27.48 r_scangle_other 18.298 r_mcangle_other 15.698 r_mcangle_it 15.695 r_dihedral_angle_3_deg 14.867 r_scbond_it 11.125 r_scbond_other 11.118 r_mcbond_it 10.201 r_mcbond_other 10.196
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 27.481 r_long_range_B_other 27.48 r_scangle_other 18.298 r_mcangle_other 15.698 r_mcangle_it 15.695 r_dihedral_angle_3_deg 14.867 r_scbond_it 11.125 r_scbond_other 11.118 r_mcbond_it 10.201 r_mcbond_other 10.196 r_dihedral_angle_2_deg 6.044 r_dihedral_angle_1_deg 4.364 r_angle_refined_deg 1.676 r_angle_other_deg 0.479 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 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 1577 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing