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crystal structure of short afifavidin - biotin complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HDS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 1.3-1.5M Ammonium Sulfate, 0.1M Acetate pH 5.0
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.131 α = 90 b = 65.218 β = 100.25 c = 67.738 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 PILATUS3 6M 2017-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.53 46.62 95.8 0.081 7 3 52210
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.53 1.59
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 6HDS 1.54 46.62 49575 2608 96.67 0.16571 0.16282 0.1721 0.22012 0.2338 RANDOM 24.1
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] 3.48 0.83 -1.76 -1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.385 r_sphericity_free 26.747 r_dihedral_angle_4_deg 17.609 r_sphericity_bonded 16.701 r_dihedral_angle_3_deg 14.134 r_dihedral_angle_1_deg 6.688 r_rigid_bond_restr 5.025 r_long_range_B_refined 4.802 r_long_range_B_other 4.766 r_scangle_other 4.574
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.385 r_sphericity_free 26.747 r_dihedral_angle_4_deg 17.609 r_sphericity_bonded 16.701 r_dihedral_angle_3_deg 14.134 r_dihedral_angle_1_deg 6.688 r_rigid_bond_restr 5.025 r_long_range_B_refined 4.802 r_long_range_B_other 4.766 r_scangle_other 4.574 r_mcangle_other 4.186 r_mcangle_it 4.185 r_scbond_other 3.893 r_scbond_it 3.891 r_mcbond_it 3.322 r_mcbond_other 3.315 r_angle_refined_deg 1.645 r_angle_other_deg 0.841 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3600 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing