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Crystal structure of the siderophore receptor PirA from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FEP PDB ENTRY 1FEP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 17% PEG 3350, 0.2 M MGCL2, 0.1 M TRIS PH 7
Crystal Properties Matthews coefficient Solvent content 2.9 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.12 α = 90 b = 95.28 β = 127.52 c = 131.83 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS 6M 2014-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 2.97 52.49 98.8 0.08 11 3.6 36861 2
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 2.97 3.05 99.9 0.62 1.8 3.8
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 1FEP 2.97 52.49 35103 1756 98.76 0.26529 0.26259 0.2619 0.31861 0.3106 RANDOM 126.995
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] -5.44 -0.52 8.88 -1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.082 r_dihedral_angle_4_deg 21.58 r_dihedral_angle_3_deg 21.022 r_dihedral_angle_1_deg 9.098 r_angle_refined_deg 1.215 r_angle_other_deg 0.71 r_chiral_restr 0.075 r_gen_planes_refined 0.015 r_bond_refined_d 0.008 r_gen_planes_other 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.082 r_dihedral_angle_4_deg 21.58 r_dihedral_angle_3_deg 21.022 r_dihedral_angle_1_deg 9.098 r_angle_refined_deg 1.215 r_angle_other_deg 0.71 r_chiral_restr 0.075 r_gen_planes_refined 0.015 r_bond_refined_d 0.008 r_gen_planes_other 0.008 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 8167 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data reduction xia2 data scaling XSCALE data scaling PHASER phasing