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The crystal structure of the ferric yersiniabactin uptake receptor FyuA from Yersinia pestis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 2.4 M ammonium formate, 0.1 M HEPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 9.03 86.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.179 α = 90 b = 181.179 β = 90 c = 319.861 γ = 90
Symmetry Space Group I 41 2 2
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 300 mm CCD 2008-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97912 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.2 50 97.9 0.25 12.4 12.7 40958 40958 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.28 83 0.25 1.5 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 3.2 50 40958 40958 2179 97.7 0.22782 0.22697 0.2219 0.24381 0.2377 RANDOM 36.823
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] 3.22 3.22 -6.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.272 r_dihedral_angle_4_deg 19.723 r_dihedral_angle_3_deg 18.481 r_scangle_it 8.199 r_dihedral_angle_1_deg 7.032 r_scbond_it 5.577 r_mcangle_it 4.187 r_mcbond_it 3.105 r_angle_refined_deg 1.44 r_angle_other_deg 0.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.272 r_dihedral_angle_4_deg 19.723 r_dihedral_angle_3_deg 18.481 r_scangle_it 8.199 r_dihedral_angle_1_deg 7.032 r_scbond_it 5.577 r_mcangle_it 4.187 r_mcbond_it 3.105 r_angle_refined_deg 1.44 r_angle_other_deg 0.828 r_mcbond_other 0.549 r_symmetry_vdw_other 0.297 r_nbd_refined 0.209 r_nbtor_refined 0.202 r_nbd_other 0.197 r_xyhbond_nbd_refined 0.172 r_symmetry_vdw_refined 0.16 r_symmetry_hbond_refined 0.115 r_nbtor_other 0.093 r_chiral_restr 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4852 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 21
Software Software Software Name Purpose SERGUI data collection SHARP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling