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Crystal structure of the triscatecholate siderophore binding protein FeuA from Bacillus subtilis
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 8 PROTEIN WAS CRYSTALLIZED FROM 30% (V/V) JEFFAMINE ED-2001 PH 7.0, 100 MM HEPES, PH 8.0; THEN SOAKED IN MOTHER LIQUOR CONTAINING 30% (V/V) GLYCEROL FOR CRYOPROTECTION
Crystal Properties Matthews coefficient Solvent content 1.92 35.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.71 α = 90 b = 54.71 β = 90 c = 177.66 γ = 90
Symmetry Space Group P 41 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 CCD ADSC CCD MIRRORS 2008-02-16 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 1.55 19.26 98.1 0.06 17.5 4.7 39175 -3 16.698
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 1.55 1.64 95.9 0.37 4.8 4.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2PHZ 1.55 19.23 38175 999 97.58 0.18267 0.18178 0.21544 0.2307 RANDOM 20.372
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] -0.25 -0.25 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.511 r_dihedral_angle_3_deg 12.687 r_dihedral_angle_4_deg 11.566 r_dihedral_angle_1_deg 5.221 r_scangle_it 3.973 r_scbond_it 2.425 r_mcangle_it 1.393 r_angle_refined_deg 1.349 r_mcbond_it 0.855 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.511 r_dihedral_angle_3_deg 12.687 r_dihedral_angle_4_deg 11.566 r_dihedral_angle_1_deg 5.221 r_scangle_it 3.973 r_scbond_it 2.425 r_mcangle_it 1.393 r_angle_refined_deg 1.349 r_mcbond_it 0.855 r_nbtor_refined 0.312 r_symmetry_hbond_refined 0.216 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.117 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_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 2198 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing