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Crystal structure of Campylobacter jejuni Cj0843c lytic transglycosylase in complex with N,N'-diacetylchitobiose
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, SITTING DROP 293 100 sodium citrate buffer pH 5.1-6.0, and 25-33% PEG 600. The protein was concentrated to 10 mg/ml in 10 mM HEPES pH 8.0 and 200 mM ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.63 66.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 176.989 α = 90 b = 176.989 β = 90 c = 176.989 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 16M 2020-08-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X17B1 0.97935 NSLS X17B1
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 2.58 29.52 99.5 0.17 0.997 13 13.9 28913
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 2.58 2.65 1.018 0.782
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 2.58 29.5 27339 1574 99.52 0.1786 0.1757 0.1803 0.2287 0.2261 RANDOM 42.196
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_2_deg 35.186 r_dihedral_angle_4_deg 18.879 r_dihedral_angle_3_deg 17.923 r_dihedral_angle_1_deg 6.159 r_angle_refined_deg 1.523 r_angle_other_deg 1.292 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.186 r_dihedral_angle_4_deg 18.879 r_dihedral_angle_3_deg 17.923 r_dihedral_angle_1_deg 6.159 r_angle_refined_deg 1.523 r_angle_other_deg 1.292 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4276 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing