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Crystal structure of soluble lytic transglycosylase Cj0843 of Campylobacter jejuni dose-response soaking with 1 mM concentration Z7285 inhibitor (no inhibitor binding observed)
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 3.67 66.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.604 α = 90 b = 177.604 β = 90 c = 177.604 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 PILATUS 6M 2021-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.2 39.71 99.9 0.109 0.112 0.026 0.999 20.6 18.1 47185
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 99.2 2.29 2.356 0.549 0.535 18.1
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 2.2 39.71 44827 2338 99.96 0.18947 0.1881 0.1963 0.21497 0.2219 RANDOM 51.437
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 16.716 r_dihedral_angle_2_deg 11.337 r_long_range_B_other 10.066 r_long_range_B_refined 10.053 r_scangle_other 8.139 r_mcangle_it 6.553 r_mcangle_other 6.552 r_dihedral_angle_1_deg 6.049 r_scbond_it 5.465 r_scbond_other 5.464
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.716 r_dihedral_angle_2_deg 11.337 r_long_range_B_other 10.066 r_long_range_B_refined 10.053 r_scangle_other 8.139 r_mcangle_it 6.553 r_mcangle_other 6.552 r_dihedral_angle_1_deg 6.049 r_scbond_it 5.465 r_scbond_other 5.464 r_mcbond_it 4.776 r_mcbond_other 4.775 r_angle_refined_deg 1.577 r_angle_other_deg 0.52 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 4251 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 13
Software Software Software Name Purpose Aimless data scaling XDS data reduction REFMAC refinement PHASER phasing