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Crystal structure of the ferric enterobactin receptor (PfeA) in complex with BCV
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 3.46 64.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.962 α = 90 b = 157.358 β = 90 c = 78.077 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 EIGER2 XE 16M 2020-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 2.711 78.679 83 0.062 1 16.9 7.5 24453
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.711 2.858 0.555
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6q5E 2.711 78.679 24453 1171 82.984 0.227 0.2258 0.2249 0.2515 0.2502 101.994
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] -0.445 -0.945 1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.687 r_dihedral_angle_4_deg 17.275 r_dihedral_angle_3_deg 17.113 r_lrange_it 12.081 r_lrange_other 12.08 r_dihedral_angle_1_deg 9.639 r_scangle_it 9.498 r_scangle_other 9.497 r_mcangle_it 9.076 r_mcangle_other 9.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.687 r_dihedral_angle_4_deg 17.275 r_dihedral_angle_3_deg 17.113 r_lrange_it 12.081 r_lrange_other 12.08 r_dihedral_angle_1_deg 9.639 r_scangle_it 9.498 r_scangle_other 9.497 r_mcangle_it 9.076 r_mcangle_other 9.075 r_scbond_it 7.134 r_scbond_other 7.122 r_mcbond_other 6.649 r_mcbond_it 6.648 r_angle_refined_deg 1.255 r_angle_other_deg 1.073 r_nbd_other 0.301 r_symmetry_nbd_refined 0.237 r_nbd_refined 0.208 r_symmetry_nbd_other 0.207 r_xyhbond_nbd_refined 0.168 r_nbtor_refined 0.166 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.049 r_symmetry_xyhbond_nbd_other 0.044 r_gen_planes_refined 0.022 r_ext_dist_refined_d 0.02 r_gen_planes_other 0.014 r_bond_refined_d 0.009 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5370 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling PHASER phasing