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The crystal structure of DfoJ, the desferrioxamine biosynthetic pathway lysine decarboxylase from the fire blight disease pathogen Erwinia amylovora
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QMA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 55% V/V polipropylene glycol 400
Crystal Properties Matthews coefficient Solvent content 3.46 64.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 269.791 α = 90 b = 269.791 β = 90 c = 56.194 γ = 120
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 2014-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 0.987 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.1 74.96 99.91 0.084 19.7 8.1 134700
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 0.633 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2QMA 2.1 233.65 253433 13243 99.91 0.16604 0.16496 0.18662 0.1989 RANDOM 30.476
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.567 r_dihedral_angle_4_deg 18.11 r_dihedral_angle_3_deg 15.595 r_long_range_B_refined 6.757 r_long_range_B_other 6.757 r_dihedral_angle_1_deg 6.684 r_scangle_other 4.751 r_mcangle_it 3.655 r_mcangle_other 3.655 r_scbond_it 3.264
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.567 r_dihedral_angle_4_deg 18.11 r_dihedral_angle_3_deg 15.595 r_long_range_B_refined 6.757 r_long_range_B_other 6.757 r_dihedral_angle_1_deg 6.684 r_scangle_other 4.751 r_mcangle_it 3.655 r_mcangle_other 3.655 r_scbond_it 3.264 r_scbond_other 3.264 r_mcbond_it 2.616 r_mcbond_other 2.616 r_angle_refined_deg 1.822 r_angle_other_deg 1.158 r_chiral_restr 0.114 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21713 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing