☰ Navigation Tabs
X ray structure of the periplasmic ligand binding protein YfeA from Yersinia pestis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.3 293.15 30-35% PEG 4000, 50mM sodium chloride, 20mM Bis-tris propane, 0.05% w/v sodium azide
Crystal Properties Matthews coefficient Solvent content 1.71 27.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.736 α = 90 b = 52.12 β = 90 c = 113.066 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 RAYONIX MX300-HS 2016-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.28281 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 1.42 50 99.7 0.098 0.051 0.981 52.8 4.6 47252 15.596
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.42 1.44 99.6 0.401 0.213 0.854 2.2 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD FREE R-VALUE 1.421 33.577 1.37 89273 3784 99.37 0.1793 0.1788 0.1792 0.1903 0.1907
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 3.705 f_angle_d 0.76 f_chiral_restr 0.078 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2154 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHASER phasing HKL-2000 data reduction SCALEPACK data scaling