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Three-dimensional structure of AIP56, a short-trip single chain AB toxin from Photobacterium damselae subsp. piscicida.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AlphaFold2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 400 mM sodium acetate, 100 mM Tris pH 8.5, 15 % PEG 4K, 10 mM Taurine
Crystal Properties Matthews coefficient Solvent content 2.57 52.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.129 α = 90 b = 193.85 β = 113.24 c = 91.616 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 6M 2015-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.972 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.54 46.28 93.4 0.163 0.182 0.081 0.992 6.7 5 52848 48.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.54 2.78 1.036 1.158 0.509 0.488
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 AlphaFold2 2.54 46.28 52848 2563 69.6 0.2417 0.2396 0.2361 0.2823 0.2876 RANDOM 65.95
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] 1.2802 2.0531 -0.254 -1.0262
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.99 t_omega_torsion 2.73 t_angle_deg 0.96 t_bond_d 0.009 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14635 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 38
Software Software Software Name Purpose BUSTER refinement PHENIX refinement XDS data reduction STARANISO data scaling PHASER phasing