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L-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) 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 0.94 41.886 93.7 0.009 1 31.4 35.1 139644
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.94 0.96 71.6 0.798 0.449 0.8 20.4
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 0.944 41.886 138990 2769 93.465 0.127 0.1262 0.133 0.1466 0.15 12.615
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] -0.439 1.456 -1.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.118 r_dihedral_angle_4_deg 21.708 r_rigid_bond_restr 13.753 r_dihedral_angle_3_deg 11.297 r_dihedral_angle_1_deg 8.198 r_lrange_it 4.287 r_lrange_other 4.286 r_mcangle_other 3.862 r_mcangle_it 3.843 r_scangle_it 3.767
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.118 r_dihedral_angle_4_deg 21.708 r_rigid_bond_restr 13.753 r_dihedral_angle_3_deg 11.297 r_dihedral_angle_1_deg 8.198 r_lrange_it 4.287 r_lrange_other 4.286 r_mcangle_other 3.862 r_mcangle_it 3.843 r_scangle_it 3.767 r_scangle_other 3.766 r_mcbond_it 3.389 r_mcbond_other 3.059 r_scbond_it 2.968 r_scbond_other 2.966 r_angle_refined_deg 2.473 r_angle_other_deg 1.121 r_chiral_restr 1.036 r_symmetry_nbd_refined 0.875 r_nbd_other 0.439 r_symmetry_xyhbond_nbd_refined 0.291 r_symmetry_nbd_other 0.218 r_nbd_refined 0.203 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.168 r_symmetry_nbtor_other 0.088 r_bond_refined_d 0.028 r_gen_planes_refined 0.015 r_symmetry_xyhbond_nbd_other 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1815 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing