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Crystal structure of the ferripyoverdine receptor of the outer membrane of Pseudomonas aeruginosa bound to ferripyoverdine.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XKH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 Na Acetate 0.1 M, pH 4.6; 12 mM MgSO4, 12 % PEG 3350.
Protein concentration in 0.5 % C8E4: 15 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.79 55.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.123 α = 90 b = 82.123 β = 90 c = 286.225 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 QUANTUM 210 2005-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97857 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.73 46.96 94.4 0.045 7.3 2.9 24636 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.73 2.88 78.3 0.274 1.3 2.2 2982
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 1XKH 2.73 46.96 23442 1193 100 0.24611 0.24412 0.2426 0.28522 0.2843 RANDOM 51.148
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] 1.61 1.61 -3.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.541 r_dihedral_angle_3_deg 16.675 r_dihedral_angle_4_deg 12.359 r_dihedral_angle_1_deg 5.192 r_angle_refined_deg 1.096 r_scangle_it 0.677 r_scbond_it 0.49 r_nbtor_refined 0.297 r_mcangle_it 0.296 r_mcbond_it 0.208
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.541 r_dihedral_angle_3_deg 16.675 r_dihedral_angle_4_deg 12.359 r_dihedral_angle_1_deg 5.192 r_angle_refined_deg 1.096 r_scangle_it 0.677 r_scbond_it 0.49 r_nbtor_refined 0.297 r_mcangle_it 0.296 r_mcbond_it 0.208 r_nbd_refined 0.186 r_symmetry_vdw_refined 0.152 r_xyhbond_nbd_refined 0.114 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5973 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing