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Crystal structure of self-complemented MyfA, the major subunit of Myf fimbriae from Yersinia enterocolitica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LND
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 35% dioxane v/v
Crystal Properties Matthews coefficient Solvent content 2.28 46.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.98 α = 90 b = 41.97 β = 90 c = 150.83 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 CCD MARMOSAIC 225 mm CCD 2013-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9737 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.8 150.83 99.9 0.085 0.099 0.049 9.6 3.7 25547 25547
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 100 0.758 0.758 0.885 0.447 1 3.7 3662
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 5LND 1.9 29.681 1.35 21748 1116 99.76 0.1623 0.1587 0.1613 0.1912 0.1684 26.61
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 15.497 f_angle_d 1.431 f_chiral_restr 0.082 f_bond_d 0.012 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1951 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction SCALA data scaling PHASER phasing PDB_EXTRACT data extraction PHENIX model building