8GFJ

Crystal structure of soluble lytic transglycosylase Cj0843 of Campylobacter jejuni dose-response soaking with 1 mM concentration Z7285 inhibitor (no inhibitor binding observed)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6CF9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.92930.1 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 coefficientSolvent content
3.6766.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.604α = 90
b = 177.604β = 90
c = 177.604γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.9795SSRLBL12-2

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.239.7199.90.1090.1120.0260.99920.618.147185
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)RedundancyNumber Unique Reflections (All)
12.22.2799.22.292.3560.5490.53518.1

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 REPLACEMENTTHROUGHOUT6CF92.239.7144827233899.960.189470.18810.21497RANDOM51.437
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
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.716
r_dihedral_angle_2_deg11.337
r_long_range_B_other10.066
r_long_range_B_refined10.053
r_scangle_other8.139
r_mcangle_it6.553
r_mcangle_other6.552
r_dihedral_angle_1_deg6.049
r_scbond_it5.465
r_scbond_other5.464
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.716
r_dihedral_angle_2_deg11.337
r_long_range_B_other10.066
r_long_range_B_refined10.053
r_scangle_other8.139
r_mcangle_it6.553
r_mcangle_other6.552
r_dihedral_angle_1_deg6.049
r_scbond_it5.465
r_scbond_other5.464
r_mcbond_it4.776
r_mcbond_other4.775
r_angle_refined_deg1.577
r_angle_other_deg0.52
r_chiral_restr0.076
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms4251
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms13

Software

Software
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
REFMACrefinement
PHASERphasing