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Complex of the Yersinia enterocolitica Type III secretion proteins YscX and YscY
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QIH D_1292118683
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Protein Concentration: 5 mg/mL;
Protein Buffer: 10 mM Tris pH 8.0, 50 mM NaCl, 5 % (w/v) sucrose, 2.5 mM TCEP;
Reservoir Solution: 0.1 M Sodium succinate pH 6-6.5, 4.2-4.4 M NaCl, 4 % acetonitrile;
Drop Ratio: 0.5 - 1 uL Reservoir + 1 uL Protein
Crystal Properties Matthews coefficient Solvent content 3.31 62.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.268 α = 90 b = 179.268 β = 90 c = 41.07 γ = 90
Symmetry Space Group I 41 2 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 PILATUS 6M 2014-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1 SLS X06SA
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 3.29 50 99.8 0.13 0.999 14.55 12.7 5368 111.44
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 3.29 3.49 99.3 1.255 0.773 2.25 13
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 D_1292118683 3.29 44.82 1.34 5357 535 99.74 0.2296 0.2237 0.2272 0.2831 0.2801 119.02
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 15.6619 f_angle_d 1.7665 f_chiral_restr 0.0879 f_plane_restr 0.0125 f_bond_d 0.0121
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1519 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing