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Crystal structure of the Secreted Extracellular protein A (SepA) from Shigella flexneri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WXR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 A 1:1 ratio of 10mg/ml protein was mixed with the following - 0.085M MES/IMID pH 6.5, 0.015M Na HEPES pH 7.5, 8.5% PEG 8K, 17% ethylene glycol, 0.03M MgCl2 and 4.5% PEG 400
Crystal Properties Matthews coefficient Solvent content 3.66 66.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.52 α = 90 b = 143.52 β = 90 c = 269.25 γ = 120
Symmetry Space Group P 32 2 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 CCD RAYONIX MX225HE 2014-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.912 72.763 100 0.32 0.3 1 7.73 10.4 70949
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.912 3 100 1.7 0.3 1.4 8.8 6981
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 1WXR 2.912 72.763 1.34 70882 3580 99.86 0.2156 0.2143 0.2173 0.2388 0.2405
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 11.01 f_angle_d 0.469 f_chiral_restr 0.042 f_plane_restr 0.003 f_bond_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15000 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 15
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction SCALA data scaling PHASER phasing