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Complex of the Yersinia enterocolitica Type III secretion export gate YscV with substrate:chaperone complex YscX:YscY
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ALW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Protein Concentration: 3-5 mg/ml;
Protein Buffer: 20 mM Tris pH 8.0, 150 mM NaCl, 5 mM TCEP;
Reservoir Solution: 0.1 M Hepes pH 6.8-8.0, 1 % PEG 2'000 MME, 0.8-1.2 M sodium succinate;
Drop Ratio: 0.33 uL Reservoir + 0.66 uL Protein
Crystal Properties Matthews coefficient Solvent content 3.75 67.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.46 α = 90 b = 324.92 β = 90 c = 369.38 γ = 90
Symmetry Space Group P 21 21 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 2018-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 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 3.7 49.83 99.5 0.17 0.998 7.1 5.2 135378 162.98
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 3.7 3.92 98.1 2.893 0.395 0.65 5.23
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 7ALW 4.1 49.83 1.34 135238 6766 99.62 0.3064 0.3054 0.3057 0.3248 0.325 193.98
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 12.4843 f_angle_d 0.6037 f_chiral_restr 0.0388 f_plane_restr 0.0039 f_bond_d 0.0023
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 73476 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction PHASER phasing XDS data scaling