5MBU | pdb_00005mbu

CeuE (H227A, 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 DROP9298=0.1M SPG, pH 9.0; 25% Peg1500.
Crystal Properties
Matthews coefficientSolvent content
2.448.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.9α = 82.23
b = 62.611β = 76.96
c = 67.792γ = 75.98
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110PIXELDECTRIS PILATUS3 6M2016-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.98DiamondI03

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
11.8165.895.90.0740.9968.83.477003
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)
11.811.8596.20.7790.5991.63.3

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3zkw1.8165.873272373195.820.201470.199550.210.238580.24RANDOM34.448
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]
-0.02-1.97-0.43-0.550.78-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.504
r_dihedral_angle_3_deg14.989
r_dihedral_angle_4_deg14.21
r_long_range_B_other6.447
r_long_range_B_refined6.446
r_dihedral_angle_1_deg6.428
r_scangle_other5.282
r_mcangle_other4.477
r_mcangle_it4.476
r_scbond_it3.674
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.504
r_dihedral_angle_3_deg14.989
r_dihedral_angle_4_deg14.21
r_long_range_B_other6.447
r_long_range_B_refined6.446
r_dihedral_angle_1_deg6.428
r_scangle_other5.282
r_mcangle_other4.477
r_mcangle_it4.476
r_scbond_it3.674
r_scbond_other3.674
r_mcbond_it3.356
r_mcbond_other3.354
r_angle_refined_deg1.961
r_angle_other_deg1.167
r_chiral_restr0.123
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.005
r_gen_planes_other0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6295
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing