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Crystal structure of the ferric enterobactin receptor (PfeA) in complex with TCV_L5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Q5E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 294 PEG 8000, ADA, Magnesium acetate
Crystal Properties Matthews coefficient Solvent content 3.32 62.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.795 α = 90 b = 157.049 β = 90 c = 77.503 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS 6M-F 2019-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.717 75.293 99.8 0.071 0.999 12.5 7.1 28920
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 2.717 2.76 93.5 1.752 0.443
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 6q5e 2.717 75.293 28865 1465 99.634 0.216 0.2144 0.258 0.2389 95.139
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] 1.126 -0.961 -0.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.36 r_dihedral_angle_4_deg 19.473 r_dihedral_angle_3_deg 17.757 r_lrange_it 9.82 r_lrange_other 9.82 r_dihedral_angle_1_deg 9.527 r_scangle_it 8.623 r_scangle_other 8.622 r_mcangle_it 7.394 r_mcangle_other 7.393
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.36 r_dihedral_angle_4_deg 19.473 r_dihedral_angle_3_deg 17.757 r_lrange_it 9.82 r_lrange_other 9.82 r_dihedral_angle_1_deg 9.527 r_scangle_it 8.623 r_scangle_other 8.622 r_mcangle_it 7.394 r_mcangle_other 7.393 r_scbond_it 6.188 r_scbond_other 6.175 r_mcbond_other 5.485 r_mcbond_it 5.484 r_angle_refined_deg 1.349 r_angle_other_deg 1.174 r_symmetry_nbd_refined 0.398 r_nbd_other 0.34 r_nbd_refined 0.208 r_symmetry_nbd_other 0.208 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.16 r_metal_ion_refined 0.079 r_symmetry_nbtor_other 0.075 r_symmetry_xyhbond_nbd_other 0.07 r_ext_dist_refined_d 0.055 r_chiral_restr 0.052 r_gen_planes_refined 0.017 r_bond_refined_d 0.007 r_gen_planes_other 0.007 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5370 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing