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Crystal Structure of the Yersinia Virulence Effector YopE Chaperone-binding Domain in Complex with its Secretion Chaperone, SycE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JYA PDB entry 1jya
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 291 PEG 8000, sodium tartrate, sodium acetate, dithiothreitol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.38 48.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.845 α = 103.37 b = 73.352 β = 109.18 c = 74.263 γ = 107.36
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2001-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.00 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.99 20 97.3 0.058 0.058 18.22 2 87145 84804 -3 36.69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.99 2.03 96.5 0.46 0.46 1.77 2 4425
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 PDB entry 1jya 2 20 84845 84804 4252 97.3 0.251 0.248 0.275 0.2714 random 5% 48.05
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] 1.81 2.387 5.289 1.204 -1.036 -3.013
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.74 c_angle_d 1.15 c_improper_angle_d 0.76 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9232 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement