6CFC

Crystal structure of soluble lytic transglycosylase Cj0843 of Campylobacter jejuni in complex with Bulgecin A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6CF8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52980.2 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 coefficientSolvent content
2.5251.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.294α = 90
b = 74.294β = 90
c = 190.461γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2017-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97946SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.0464.3499.111.65.739342
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.042.09

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6CF82.0464.3437371192099.080.17930.17730.2199RANDOM42.486
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.127
r_dihedral_angle_3_deg14.078
r_dihedral_angle_4_deg13.595
r_dihedral_angle_1_deg5.27
r_angle_refined_deg1.314
r_angle_other_deg0.977
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.127
r_dihedral_angle_3_deg14.078
r_dihedral_angle_4_deg13.595
r_dihedral_angle_1_deg5.27
r_angle_refined_deg1.314
r_angle_other_deg0.977
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4192
Nucleic Acid Atoms
Solvent Atoms291
Heterogen Atoms80

Software

Software
Software NamePurpose
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
MOLREPphasing