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Crystal Structure of a Sugar N-Formyltransferase from the Plant Pathogen Pantoea ananatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YFV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 13-16%PEG-3350, 2 mM folinic acid, 5 mM dTDP-Qui4N, 200 mM NaCl, 100 mM HEPES
Crystal Properties Matthews coefficient Solvent content 2.43 49.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.928 α = 90 b = 75.928 β = 90 c = 87.591 γ = 120
Symmetry Space Group P 31 2 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 2018-04-05 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 1.7 50 98.3 0.061 0.061 13.1 7.6 32264
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 1.7 1.8 94.1 0.433 0.433 2.1 3.7
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 4YFV 1.7 50 30727 1537 98.29 0.18764 0.18574 0.1931 0.22646 0.2319 RANDOM 26.513
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] 0.48 0.24 0.48 -1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.091 r_dihedral_angle_4_deg 21.798 r_dihedral_angle_3_deg 16.251 r_dihedral_angle_1_deg 6.786 r_long_range_B_refined 6.407 r_long_range_B_other 6.312 r_scangle_other 4.395 r_mcangle_it 3.39 r_mcangle_other 3.388 r_scbond_it 2.875
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.091 r_dihedral_angle_4_deg 21.798 r_dihedral_angle_3_deg 16.251 r_dihedral_angle_1_deg 6.786 r_long_range_B_refined 6.407 r_long_range_B_other 6.312 r_scangle_other 4.395 r_mcangle_it 3.39 r_mcangle_other 3.388 r_scbond_it 2.875 r_scbond_other 2.82 r_mcbond_it 2.248 r_mcbond_other 2.247 r_angle_refined_deg 1.554 r_angle_other_deg 0.504 r_chiral_restr 0.068 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 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 1966 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing