5LWH

CeuE (Y288F variant) a periplasmic protein from Campylobacter jejuni.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZKW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62980.01M ZnCl2; 0.1M MES, pH 6.0; 20% Peg 6000
Crystal Properties
Matthews coefficientSolvent content
2.8356.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.521α = 90
b = 65.521β = 90
c = 145.654γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.979DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.4756.811000.045121.79.762481
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)RedundancyNumber Unique Reflections (All)
11.471.51001.2670.6351.88.9

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 REPLACEMENTTHROUGHOUT3ZKW1.4756.8159367311499.950.13010.128430.16196RANDOM26.628
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_deg38.779
r_sphericity_free26.024
r_sphericity_bonded15.531
r_dihedral_angle_3_deg12.87
r_dihedral_angle_4_deg8.16
r_scangle_other7.649
r_scbond_other6.895
r_scbond_it6.892
r_long_range_B_other6.635
r_long_range_B_refined6.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.779
r_sphericity_free26.024
r_sphericity_bonded15.531
r_dihedral_angle_3_deg12.87
r_dihedral_angle_4_deg8.16
r_scangle_other7.649
r_scbond_other6.895
r_scbond_it6.892
r_long_range_B_other6.635
r_long_range_B_refined6.63
r_rigid_bond_restr6.038
r_dihedral_angle_1_deg5.733
r_mcangle_it3.872
r_mcangle_other3.871
r_mcbond_other3.318
r_mcbond_it3.317
r_angle_refined_deg2.456
r_angle_other_deg1.362
r_chiral_restr0.189
r_bond_refined_d0.03
r_gen_planes_refined0.013
r_gen_planes_other0.004
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2231
Nucleic Acid Atoms
Solvent Atoms186
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing