6CF9

Crystal structure of soluble lytic transglycosylase Cj0843 of Campylobacter jejuni at 2.3A resolution in I23 space group


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62980.2 M Ammonium acetate, 0.1 M sodium acetate pH 4.6, and 30% (w/v) PEG 4000
Crystal Properties
Matthews coefficientSolvent content
3.9268.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.674α = 90
b = 178.674β = 90
c = 178.674γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2017-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97940SSRLBL9-2

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
12.28126.3499.621.540.442902
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.282.35

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 REPLACEMENTTHROUGHOUT6CF82.29126.3440096208698.670.20140.19970.2321RANDOM62.451
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.601
r_dihedral_angle_4_deg16.935
r_dihedral_angle_3_deg14.345
r_dihedral_angle_1_deg5.133
r_angle_refined_deg1.286
r_angle_other_deg0.93
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.601
r_dihedral_angle_4_deg16.935
r_dihedral_angle_3_deg14.345
r_dihedral_angle_1_deg5.133
r_angle_refined_deg1.286
r_angle_other_deg0.93
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4276
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms16

Software

Software
Software NamePurpose
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
MOLREPphasing