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Heterologous Complex of shortened Aeromonas hydrophila Type III secretion substrate AscX with Yersinia enterocolitica chaperone YscY
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QIH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 reservoir solution: 0.1 M Hepes pH 7.5, 0.6-0.9 M sodium dihydrogen phosphate, 0.6-0.9 M potassium dihydrogen phosphate [1.4-1.8 M total phosphate];
protein: 10 mg/mL in 20 mM Tris pH 8, 150 mM NaCl, 5 mM TCEP;
drop size: 0.66 uL protein + 0.33 uL reservoir
Crystal Properties Matthews coefficient Solvent content 3.19 61.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.33 α = 90 b = 160.56 β = 90 c = 156.74 γ = 90
Symmetry Space Group C 2 2 21
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-F 2020-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9919 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.63 80.28 99.3 0.229 0.996 9.3 24.86 34253 80.05
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.63 2.7 92.6 4.831 0.239 0.61 12.93
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7QIH 2.63 80.28 1.33 33394 1664 97.98 0.293 0.2912 0.3009 0.3262 0.3339 108.73
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.5589 f_angle_d 0.3579 f_chiral_restr 0.0279 f_plane_restr 0.0028 f_bond_d 0.0017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5266 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 35
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement