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X-ray structure of the FdtF formyltransferase from salmonella enteric O60 in complex with TDP-Fuc3N and folinic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UIJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 100 mM CHES
12-16% PEG 5000
200 mM NMe4Cl
10 mM folinic acid
10 mM TDP-Fuc3N
Crystal Properties Matthews coefficient Solvent content 2.48 50.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.237 α = 90 b = 69.199 β = 90 c = 200.641 γ = 90
Symmetry Space Group P 21 21 21
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 Bruker Platinum 135 montel 2016-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 50 97.2 0.095 0.095 7.9 4.1 46716
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.3 91.3 0.364 0.364 2 2.3
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 5UIJ 2.2 48.09 44292 2366 97.27 0.20931 0.20604 0.2103 0.27083 0.2702 RANDOM 28.844
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] 1.23 -0.08 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.919 r_dihedral_angle_4_deg 18.848 r_dihedral_angle_3_deg 16.903 r_dihedral_angle_1_deg 6.772 r_long_range_B_refined 5.27 r_long_range_B_other 5.253 r_scangle_other 3.705 r_mcangle_it 2.958 r_mcangle_other 2.958 r_scbond_it 2.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.919 r_dihedral_angle_4_deg 18.848 r_dihedral_angle_3_deg 16.903 r_dihedral_angle_1_deg 6.772 r_long_range_B_refined 5.27 r_long_range_B_other 5.253 r_scangle_other 3.705 r_mcangle_it 2.958 r_mcangle_other 2.958 r_scbond_it 2.256 r_scbond_other 2.256 r_mcbond_it 1.873 r_mcbond_other 1.873 r_angle_refined_deg 1.681 r_angle_other_deg 0.972 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 6468 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 192
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing