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X-ray structure of the FdtF N-formyltransferase from salmonella enteric O60 in complex with folinic acid and TDP-Qui3N
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
200 mM NMe4Cl
13-17% PEG 5000
10 mM folinic acid
10 mM TDP-Qui3N
Crystal Properties Matthews coefficient Solvent content 2.38 48.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.236 α = 90 b = 58.406 β = 96.04 c = 106.781 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 Bruker Platinum 135 montel 2016-06-06 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 95.2 0.084 0.084 9.3 3.7 42547
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 86.6 0.295 0.295 1.9 1.7
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 50 40390 2149 95.18 0.19799 0.19451 0.2011 0.264 0.2657 RANDOM 32.471
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] -0.19 -1.11 2.01 -1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.769 r_dihedral_angle_4_deg 22.765 r_dihedral_angle_3_deg 18.315 r_dihedral_angle_1_deg 7.511 r_long_range_B_refined 6.898 r_long_range_B_other 6.898 r_scangle_other 5.138 r_mcangle_other 4.033 r_mcangle_it 4.032 r_scbond_it 3.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.769 r_dihedral_angle_4_deg 22.765 r_dihedral_angle_3_deg 18.315 r_dihedral_angle_1_deg 7.511 r_long_range_B_refined 6.898 r_long_range_B_other 6.898 r_scangle_other 5.138 r_mcangle_other 4.033 r_mcangle_it 4.032 r_scbond_it 3.342 r_scbond_other 3.279 r_mcbond_it 2.673 r_mcbond_other 2.673 r_angle_refined_deg 1.699 r_angle_other_deg 0.902 r_chiral_restr 0.097 r_bond_refined_d 0.013 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 6464 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 169
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing