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Streptavidin K121M 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 6.5 293 1 M Na3 citrate, 0.1 M Na cacodylate pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.96 37.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.832 α = 90 b = 57.832 β = 90 c = 77.739 γ = 90
Symmetry Space Group P 42 21 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 XE 16M 2024-12-09 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 40.89 99.59 0.03391 0.04796 0.03391 0.999 11.84 2 9404
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 2.071 99.78 0.6065 0.8577 0.6065 0.756 1.25 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 40.89 8946 458 99.85 0.22722 0.2248 0.2535 0.27757 0.3 47.844
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] -3.65 -3.65 7.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.484 r_long_range_B_other 10.235 r_long_range_B_refined 10.224 r_dihedral_angle_1_deg 7.983 r_scangle_other 7.634 r_mcangle_it 6.39 r_mcangle_other 6.387 r_scbond_it 5.18 r_scbond_other 5.175 r_mcbond_it 4.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.484 r_long_range_B_other 10.235 r_long_range_B_refined 10.224 r_dihedral_angle_1_deg 7.983 r_scangle_other 7.634 r_mcangle_it 6.39 r_mcangle_other 6.387 r_scbond_it 5.18 r_scbond_other 5.175 r_mcbond_it 4.344 r_mcbond_other 4.342 r_dihedral_angle_2_deg 3.092 r_angle_refined_deg 1.787 r_angle_other_deg 0.648 r_chiral_restr 0.089 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 927 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing