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Crystal structure of the triscatecholate siderophore binding protein FeuA from Bacillus subtilis complexed with Ferri-Bacillibactin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PHZ PDB ENTRY 2PHZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.2 PROTEIN WAS CRYSTALLIZED FROM 30% (V/V) PEG 600, 100 MM PHOSPHATE-CITRATE, PH 5.2; THEN SOAKED IN MOTHER LIQUOR CONTAINING 30% (V/V) GLYCEROL FOR CRYO PROTECTION.
Crystal Properties Matthews coefficient Solvent content 1.86 33.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.53 α = 90 b = 63.14 β = 110.44 c = 55.53 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 100 CCD ADSC CCD MIRRORS 2008-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.7 19.76 99.2 0.04 20.1 3.7 28022 -3 24.416
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 1.7 1.79 99.5 0.52 3.4 3.7
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2PHZ 1.7 19.51 25537 2472 99.21 0.16042 0.15749 0.1683 0.1912 0.1983 RANDOM 23.303
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] 0.14 -0.57 -1.08 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.67 r_dihedral_angle_3_deg 13.482 r_dihedral_angle_4_deg 9.408 r_dihedral_angle_1_deg 5.096 r_scangle_it 2.275 r_scbond_it 1.45 r_angle_refined_deg 1.159 r_angle_other_deg 0.864 r_mcangle_it 0.85 r_mcbond_it 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.67 r_dihedral_angle_3_deg 13.482 r_dihedral_angle_4_deg 9.408 r_dihedral_angle_1_deg 5.096 r_scangle_it 2.275 r_scbond_it 1.45 r_angle_refined_deg 1.159 r_angle_other_deg 0.864 r_mcangle_it 0.85 r_mcbond_it 0.55 r_symmetry_vdw_other 0.228 r_nbd_refined 0.21 r_nbd_other 0.186 r_nbtor_refined 0.176 r_symmetry_hbond_refined 0.161 r_nbtor_other 0.157 r_symmetry_vdw_refined 0.141 r_mcbond_other 0.136 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.064 r_bond_refined_d 0.009 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2199 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing