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Biotin-streptavidin binding
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RY1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 294 1 micro-liter protein containing 3 mM Biotin in 10 mM Tris-HCl pH 7.0 mixed with 1 micro-liter 38% Ammonium Sulfate, 100 mM Na-Acetate pH 4.5, 200 mM NaCl at 21C (294 K)
Crystal Properties Matthews coefficient Solvent content 2.18 43.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.688 α = 90 b = 94.415 β = 90 c = 105.14 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 PILATUS 6M 2022-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9600 SSRL BL9-2
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 0.95 41.94 96.8 0.067 0.067 0.01 1 31.7 35 140605
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 0.95 0.97 79.3 3.066 3.156 0.718 0.354 18.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 0.953 41.886 139680 2793 96.626 0.131 0.131 0.1316 0.1454 0.1463 11.402
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] 0.285 -0.515 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.795 r_dihedral_angle_4_deg 18.883 r_dihedral_angle_3_deg 11.696 r_dihedral_angle_1_deg 7.74 r_rigid_bond_restr 5.315 r_lrange_it 2.3 r_lrange_other 1.987 r_angle_refined_deg 1.98 r_mcangle_other 1.933 r_mcangle_it 1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.795 r_dihedral_angle_4_deg 18.883 r_dihedral_angle_3_deg 11.696 r_dihedral_angle_1_deg 7.74 r_rigid_bond_restr 5.315 r_lrange_it 2.3 r_lrange_other 1.987 r_angle_refined_deg 1.98 r_mcangle_other 1.933 r_mcangle_it 1.93 r_scangle_other 1.775 r_scangle_it 1.774 r_mcbond_it 1.544 r_mcbond_other 1.528 r_scbond_it 1.446 r_scbond_other 1.445 r_symmetry_nbd_refined 0.975 r_angle_other_deg 0.74 r_nbd_other 0.431 r_symmetry_xyhbond_nbd_refined 0.238 r_nbd_refined 0.222 r_symmetry_nbd_other 0.218 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.118 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.025 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_xyhbond_nbd_other 0.011 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1815 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PDB_EXTRACT data extraction REFMAC phasing