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streptavidin with an iridium catalyst for CH activation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BC3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 293 2 M ammonium sulfate
0.1 M sodium acetate
(soaking at pH 6.0)
Crystal Properties Matthews coefficient Solvent content 2.92 57.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.657 α = 90 b = 57.657 β = 90 c = 183.626 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 EIGER X 16M 2022-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99988 SLS X06SA
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 1.486 45.949 99.9 0.073 0.076 0.02 1 23.7 25.3 26068
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 1.49 1.51 2.237 2.357 0.722 0.556 19.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 2BC3 1.486 45.949 25913 1366 99.348 0.174 0.1729 0.173 0.1945 0.192 24.472
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] -0.47 -0.47 0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.708 r_dihedral_angle_3_deg 11.628 r_dihedral_angle_1_deg 7.293 r_lrange_it 6.591 r_lrange_other 6.568 r_dihedral_angle_2_deg 5.907 r_scangle_it 5.294 r_scangle_other 4.991 r_scbond_it 3.421 r_scbond_other 3.208
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.708 r_dihedral_angle_3_deg 11.628 r_dihedral_angle_1_deg 7.293 r_lrange_it 6.591 r_lrange_other 6.568 r_dihedral_angle_2_deg 5.907 r_scangle_it 5.294 r_scangle_other 4.991 r_scbond_it 3.421 r_scbond_other 3.208 r_mcangle_it 3.182 r_mcangle_other 3.18 r_mcbond_it 2.162 r_mcbond_other 2.161 r_angle_refined_deg 1.882 r_angle_other_deg 0.623 r_symmetry_nbd_refined 0.235 r_nbd_refined 0.213 r_symmetry_nbd_other 0.204 r_nbd_other 0.189 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.177 r_symmetry_xyhbond_nbd_refined 0.104 r_symmetry_xyhbond_nbd_other 0.091 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.009 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 924 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Coot model building PHASER phasing Aimless data scaling