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Crystal structure of the ferric enterobactin esterase (PfeE) from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GZR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 294 PEG MME 2000, Sodium acetate, potassium nitrate
Crystal Properties Matthews coefficient Solvent content 1.92 35.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.34 α = 90 b = 111.1 β = 105.47 c = 48.5 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 RIGAKU SATURN 944+ 2016-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 55.55 96.6 0.05 0.999 17.3 3.6 30184
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 75.9 0.209 0.93 4.6 2.4
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 2gzr 2 55.55 28603 1555 96.45 0.17807 0.17561 0.22198 0.2129 RANDOM 36.902
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] 0.29 -1.08 0.01 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.643 r_dihedral_angle_4_deg 20.822 r_dihedral_angle_3_deg 14.991 r_dihedral_angle_1_deg 6.937 r_long_range_B_refined 4.665 r_long_range_B_other 4.66 r_scangle_other 3.389 r_mcangle_it 2.537 r_mcangle_other 2.536 r_scbond_it 2.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.643 r_dihedral_angle_4_deg 20.822 r_dihedral_angle_3_deg 14.991 r_dihedral_angle_1_deg 6.937 r_long_range_B_refined 4.665 r_long_range_B_other 4.66 r_scangle_other 3.389 r_mcangle_it 2.537 r_mcangle_other 2.536 r_scbond_it 2.19 r_scbond_other 2.185 r_mcbond_it 1.756 r_mcbond_other 1.755 r_angle_refined_deg 1.334 r_angle_other_deg 0.709 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3962 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing