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X-ray structure of a sugar N-formyltransferase from Shewanella sp FDAARGOS_354
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YFY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 9-14% PEG-5000, 200 mM N(C2H5)4Cl, 5 mM TDP-Qui4N, 5 mM folinic acid
Crystal Properties Matthews coefficient Solvent content 2.62 53.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.966 α = 90 b = 202.472 β = 90 c = 74.439 γ = 90
Symmetry Space Group C 2 2 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 ADSC QUANTUM 210r 2019-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9876 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 94.8 0.031 56.8 5.4 45110
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 86.1 0.155 5.6 3.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4yfy 1.9 27.1 42853 2257 94.6 0.1872 0.1842 0.2449 0.2575 RANDOM 37.676
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] 1.22 -2.4 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.203 r_dihedral_angle_4_deg 22.35 r_dihedral_angle_3_deg 15.319 r_dihedral_angle_1_deg 7.068 r_angle_refined_deg 1.633 r_angle_other_deg 1.313 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.203 r_dihedral_angle_4_deg 22.35 r_dihedral_angle_3_deg 15.319 r_dihedral_angle_1_deg 7.068 r_angle_refined_deg 1.633 r_angle_other_deg 1.313 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3993 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing