☰ Navigation Tabs
Crystal structure of soluble lytic transglycosylase Cj0843 of Campylobacter jejuni in complex with zanamivir amine inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CF9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 293 0.1 M sodium citrate pH 5.9 and 26% (v/v) PEG 600. Protein buffer was 10 mM HEPES pH 8.0, 200 mM ammonium acetate buffer
Crystal Properties Matthews coefficient Solvent content 3.7 66.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.064 α = 90 b = 178.064 β = 90 c = 178.064 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2021-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9201 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.38 29.68 99.8 0.094 0.999 25.1 20.7 37795
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.38 2.44 98.1 0.795 0.887 3.6 19.6
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 6CF9 2.38 29.68 35863 1932 99.8 0.1758 0.1737 0.1822 0.2138 0.2186 RANDOM 49.425
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.929 r_dihedral_angle_2_deg 10.617 r_dihedral_angle_1_deg 6.348 r_angle_refined_deg 1.633 r_angle_other_deg 0.603 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_bond_other_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4242 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 33
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing