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The Crystal structure of wt apo agroavidin - biotin complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Rhizavidin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 25% PEG 3350, 0.1 M MgCl2 and 0.1 M Bis Tris pH 6.0
Crystal Properties Matthews coefficient Solvent content 1.87 34.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.089 α = 90 b = 82.34 β = 90 c = 67.314 γ = 90
Symmetry Space Group P 21 21 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 2018-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.972 ESRF ID23-1
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 1.9 43.72 99.5 0.084 0.99 8.3 3.9 35567
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 1.9 1.94 99.7 0.978 0.64 4.1
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 Rhizavidin 1.9 43.72 32452 1711 95.49 0.21773 0.21488 0.2201 0.274 0.2761 RANDOM 33.817
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] -0.04 0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.9 r_dihedral_angle_4_deg 14.311 r_dihedral_angle_3_deg 14.162 r_dihedral_angle_1_deg 7.675 r_long_range_B_other 5.913 r_long_range_B_refined 5.912 r_scangle_other 4.165 r_mcangle_it 3.923 r_mcangle_other 3.922 r_scbond_it 2.761
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.9 r_dihedral_angle_4_deg 14.311 r_dihedral_angle_3_deg 14.162 r_dihedral_angle_1_deg 7.675 r_long_range_B_other 5.913 r_long_range_B_refined 5.912 r_scangle_other 4.165 r_mcangle_it 3.923 r_mcangle_other 3.922 r_scbond_it 2.761 r_scbond_other 2.76 r_mcbond_it 2.598 r_mcbond_other 2.595 r_angle_refined_deg 1.549 r_angle_other_deg 1.327 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.005 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 3596 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing