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Streptavidin K121W with a thiophenol cofactor as artificial hydrogen atom transferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZOF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 10 % w/v PEG 1K, 10 % w/v PEG 8K
Crystal Properties Matthews coefficient Solvent content 2.23 44.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.245 α = 90 b = 89.026 β = 96.9 c = 57.891 γ = 90
Symmetry Space Group C 1 2 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 PILATUS3 6M 2024-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.6199 Diamond I24
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 2.3 43.22 99.9 0.06073 0.08589 0.06073 0.997 9.28 2 25882
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 2.3 2.382 99.92 0.4825 0.6824 0.4825 0.694 1.71 2
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.3 43.22 24626 1258 99.9 0.2001 0.19737 0.2082 0.25388 0.2529 45.262
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] 0.03 -0.01 -0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.489 r_dihedral_angle_2_deg 10.865 r_long_range_B_other 10.081 r_long_range_B_refined 10.077 r_dihedral_angle_1_deg 8.038 r_scangle_other 7.144 r_mcangle_it 6.554 r_mcangle_other 6.552 r_scbond_it 4.758 r_scbond_other 4.757
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.489 r_dihedral_angle_2_deg 10.865 r_long_range_B_other 10.081 r_long_range_B_refined 10.077 r_dihedral_angle_1_deg 8.038 r_scangle_other 7.144 r_mcangle_it 6.554 r_mcangle_other 6.552 r_scbond_it 4.758 r_scbond_other 4.757 r_mcbond_it 4.294 r_mcbond_other 4.293 r_angle_refined_deg 1.742 r_angle_other_deg 0.594 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 3767 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing