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X-ray structure of the N-formyltransferase QdtF from Providencia alcalifaciens, W305A mutant, in the presence of TDP-Qui3N and N5-THF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XCZ PDB entry 4XCZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 5-7% PEG 8000, 100 mM HEPPS, 200 mM NaCl, 200 mM KCl, 5 mM TDP, 5 mM N5-THF
Crystal Properties Matthews coefficient Solvent content 2.4 48.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.279 α = 90 b = 78.279 β = 90 c = 151.105 γ = 90
Symmetry Space Group P 41 21 2
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 2014-08-27 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 1.5 50 97 0.069 0.069 11.2 4.6 73582 73582
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.54 90.5 0.364 2.3 2.5
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 PDB entry 4XCZ 1.5 35.03 69887 3695 97.01 0.18124 0.17981 0.1894 0.20828 0.2155 RANDOM 18.299
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] 0.55 0.55 -1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.08 r_dihedral_angle_4_deg 14.143 r_dihedral_angle_3_deg 12.942 r_dihedral_angle_1_deg 6.479 r_angle_refined_deg 2.084 r_angle_other_deg 0.932 r_chiral_restr 0.126 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.08 r_dihedral_angle_4_deg 14.143 r_dihedral_angle_3_deg 12.942 r_dihedral_angle_1_deg 6.479 r_angle_refined_deg 2.084 r_angle_other_deg 0.932 r_chiral_restr 0.126 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.001 r_bond_other_d 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3227 Nucleic Acid Atoms Solvent Atoms 605 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing