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dithiol-ligand bound to streptavidin
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 7 298 0.1 M MIB, 25 % w/v PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.27 45.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.324 α = 90 b = 80.79 β = 104.317 c = 46.657 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 PILATUS 2M-F 2021-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.999997 SLS X06DA
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 1.45 45.249 97.4 0.079 0.094 0.05 0.998 11.7 6.7 50291
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 1.45 1.47 0.886 1.046 0.553 0.78 6.7
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 FREE R-VALUE 2bc3 1.45 45.249 50261 2449 97.168 0.181 0.1799 0.1787 0.204 0.2033 18.912
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] -0.741 0.694 -0.474 0.761
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.6 r_dihedral_angle_6_deg 16.857 r_dihedral_angle_3_deg 14.255 r_dihedral_angle_1_deg 7.507 r_lrange_it 6.718 r_lrange_other 6.639 r_scangle_it 4.899 r_scangle_other 4.898 r_scbond_it 3.419 r_scbond_other 3.419
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.6 r_dihedral_angle_6_deg 16.857 r_dihedral_angle_3_deg 14.255 r_dihedral_angle_1_deg 7.507 r_lrange_it 6.718 r_lrange_other 6.639 r_scangle_it 4.899 r_scangle_other 4.898 r_scbond_it 3.419 r_scbond_other 3.419 r_mcangle_it 3.18 r_mcangle_other 3.18 r_mcbond_other 2.149 r_mcbond_it 2.147 r_angle_refined_deg 1.812 r_angle_other_deg 0.749 r_symmetry_nbd_refined 0.258 r_nbd_refined 0.228 r_symmetry_xyhbond_nbd_refined 0.212 r_symmetry_nbd_other 0.203 r_xyhbond_nbd_refined 0.19 r_nbtor_refined 0.185 r_nbd_other 0.17 r_chiral_restr 0.122 r_symmetry_xyhbond_nbd_other 0.09 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1836 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building Aimless data scaling PDB_EXTRACT data extraction PHASER phasing