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Crystal structure of soluble lytic transglycosylase Cj0843 of Campylobacter jejuni in complex with Bulgecin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CF8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5 and 25% (w/v) PEG 3350. Bulgecin A was soaked into the crystal at 2.4mM concentration for 40 min at room temperature prior to freezing the crystal
Crystal Properties Matthews coefficient Solvent content 2.52 51.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.294 α = 90 b = 74.294 β = 90 c = 190.461 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 PIXEL DECTRIS PILATUS3 S 6M 2017-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.04 64.34 99.1 11.6 5.7 39342
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.09
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 6CF8 2.04 64.34 37371 1920 99.08 0.1793 0.1773 0.1866 0.2199 0.2284 RANDOM 42.486
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.127 r_dihedral_angle_3_deg 14.078 r_dihedral_angle_4_deg 13.595 r_dihedral_angle_1_deg 5.27 r_angle_refined_deg 1.314 r_angle_other_deg 0.977 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.127 r_dihedral_angle_3_deg 14.078 r_dihedral_angle_4_deg 13.595 r_dihedral_angle_1_deg 5.27 r_angle_refined_deg 1.314 r_angle_other_deg 0.977 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4192 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 80
Software Software Software Name Purpose XDS data reduction REFMAC refinement PDB_EXTRACT data extraction XDS data scaling MOLREP phasing