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X-ray structure of The FdtF N-formyltransferase from Salmonella enteric O60 in complex with TDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XCZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 100 mM MOPS
15-18% PEG 3350
5 mM TDP
Crystal Properties Matthews coefficient Solvent content 2.54 51.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.91 α = 90 b = 64.757 β = 90.54 c = 97.757 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 2016-05-05 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 1.9 97.75 95.6 0.063 0.063 12.6 3.7 70013
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 1.9 2 87.2 0.278 0.278 2.5 1.8
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 4xcz 1.9 97.75 66447 3552 95.56 0.18332 0.18081 0.1901 0.23126 0.2387 RANDOM 26.351
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] -0.24 0.52 1.44 -1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.195 r_dihedral_angle_4_deg 18.077 r_dihedral_angle_3_deg 17.043 r_dihedral_angle_1_deg 7.203 r_long_range_B_refined 7.099 r_long_range_B_other 7.099 r_scangle_other 5.848 r_scbond_it 4.058 r_scbond_other 4.058 r_mcangle_it 3.465
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.195 r_dihedral_angle_4_deg 18.077 r_dihedral_angle_3_deg 17.043 r_dihedral_angle_1_deg 7.203 r_long_range_B_refined 7.099 r_long_range_B_other 7.099 r_scangle_other 5.848 r_scbond_it 4.058 r_scbond_other 4.058 r_mcangle_it 3.465 r_mcangle_other 3.465 r_mcbond_it 2.679 r_mcbond_other 2.679 r_angle_refined_deg 1.995 r_angle_other_deg 0.944 r_chiral_restr 0.124 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 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 6463 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing