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Crystal structure of siderophore binding protein VatD from Vibrio vulnificus M2799 complexed with Desferal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EFD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 30%(w/v) PEG-3,350, 50mM MgCl2, 0.1M Bis-Tris pH6.5
Crystal Properties Matthews coefficient Solvent content 2.02 39.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.8 α = 90 b = 57.89 β = 95.02 c = 62.7 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 130 IMAGE PLATE RIGAKU RAXIS VII 2021-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.85 26.3 97.6 0.085 10.6 3.48 20814
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 0.345
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 FREE R-VALUE 1EFD 1.9 26.103 19251 982 97.775 0.179 0.1765 0.1867 0.2187 0.2244 25.187
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] -0.017 -0.009 0.004 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.234 r_dihedral_angle_4_deg 25.54 r_dihedral_angle_3_deg 15.324 r_dihedral_angle_1_deg 6.212 r_lrange_it 6.099 r_lrange_other 6.085 r_scangle_it 4.868 r_scangle_other 4.866 r_scbond_it 3.039 r_scbond_other 3.037
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.234 r_dihedral_angle_4_deg 25.54 r_dihedral_angle_3_deg 15.324 r_dihedral_angle_1_deg 6.212 r_lrange_it 6.099 r_lrange_other 6.085 r_scangle_it 4.868 r_scangle_other 4.866 r_scbond_it 3.039 r_scbond_other 3.037 r_mcangle_it 2.67 r_mcangle_other 2.67 r_mcbond_it 1.861 r_mcbond_other 1.845 r_angle_refined_deg 1.628 r_angle_other_deg 1.377 r_symmetry_xyhbond_nbd_refined 0.279 r_nbd_refined 0.204 r_symmetry_nbd_refined 0.201 r_symmetry_nbd_other 0.184 r_nbd_other 0.178 r_nbtor_refined 0.159 r_xyhbond_nbd_refined 0.157 r_xyhbond_nbd_other 0.146 r_chiral_restr 0.127 r_symmetry_nbtor_other 0.078 r_metal_ion_refined 0.043 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2174 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling MOLREP phasing