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The Crystal structure of short F46Y agroavidin - apo
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8ASR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 18% pentaerythritol ethoxylate, 0.05 M Bis Tris pH 6.0, 0.05 M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.16 43.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.626 α = 90 b = 84.66 β = 90 c = 68.107 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 EIGER2 S 16M 2018-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0723 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.55 52.56 94.7 0.993 8.6 4.7 66081
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.59 0.469 1.2
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 8ASR 1.55 52.55 62725 3277 94.31 0.20516 0.2034 0.2114 0.23779 0.2454 RANDOM 24.433
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] -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.117 r_dihedral_angle_4_deg 14.796 r_dihedral_angle_3_deg 14.776 r_dihedral_angle_1_deg 7.018 r_long_range_B_refined 6.529 r_long_range_B_other 6.498 r_scangle_other 4.942 r_mcangle_it 3.356 r_mcangle_other 3.356 r_scbond_it 3.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.117 r_dihedral_angle_4_deg 14.796 r_dihedral_angle_3_deg 14.776 r_dihedral_angle_1_deg 7.018 r_long_range_B_refined 6.529 r_long_range_B_other 6.498 r_scangle_other 4.942 r_mcangle_it 3.356 r_mcangle_other 3.356 r_scbond_it 3.335 r_scbond_other 3.333 r_mcbond_it 2.264 r_mcbond_other 2.251 r_angle_refined_deg 1.741 r_angle_other_deg 1.54 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 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 3426 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing