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Structure of short biotin complexed agroavidin with the Hoef tail.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8AST
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% ethylene glycol
0.05M acetic acid pH 3.2
Crystal Properties Matthews coefficient Solvent content 3.27 62.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.106 α = 90 b = 81.576 β = 114.87 c = 170.05 γ = 90
Symmetry Space Group P 1 21 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 2020-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.965 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.87 50 99.3 0.089 0.993 6.8 3.35 74109
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.87 2.96 0.932 0.465
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 8AST 2.87 50 74109 4024 94.99 0.23446 0.23103 0.234 0.29716 0.2941 RANDOM
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] -0.1 0.01 0.02 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.269 r_dihedral_angle_3_deg 19.236 r_long_range_B_refined 14.899 r_long_range_B_other 14.899 r_dihedral_angle_4_deg 14.268 r_mcangle_it 9.623 r_mcangle_other 9.623 r_scangle_other 9.058 r_dihedral_angle_1_deg 7.94 r_mcbond_it 6.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.269 r_dihedral_angle_3_deg 19.236 r_long_range_B_refined 14.899 r_long_range_B_other 14.899 r_dihedral_angle_4_deg 14.268 r_mcangle_it 9.623 r_mcangle_other 9.623 r_scangle_other 9.058 r_dihedral_angle_1_deg 7.94 r_mcbond_it 6.197 r_mcbond_other 6.19 r_scbond_it 5.846 r_scbond_other 5.845 r_angle_refined_deg 1.634 r_angle_other_deg 1.223 r_chiral_restr 0.061 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.001 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 17840 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 320
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction XDS data scaling PHASER phasing