5MBQ | pdb_00005mbq

CeuE (H227A 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 DROP92980.1M MMT buffer, 25% Peg 1500.
Crystal Properties
Matthews coefficientSolvent content
2.3948.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.988α = 82.11
b = 62.682β = 77.21
c = 67.969γ = 76.28
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
11.3366.0265.90.00440.99811.83.3192548
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)
11.331.35410.7290.6041.43

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 REPLACEMENTTHROUGHOUT3ZKW1.3366.02168875893287.170.150130.147860.150.193130.2RANDOM24.583
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]
-1.031.25-0.971.09-1.04-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.4
r_sphericity_free29.77
r_dihedral_angle_4_deg20.675
r_sphericity_bonded17.9
r_dihedral_angle_3_deg12.841
r_rigid_bond_restr6.166
r_dihedral_angle_1_deg6.045
r_scangle_other5.632
r_long_range_B_refined5.355
r_long_range_B_other5.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.4
r_sphericity_free29.77
r_dihedral_angle_4_deg20.675
r_sphericity_bonded17.9
r_dihedral_angle_3_deg12.841
r_rigid_bond_restr6.166
r_dihedral_angle_1_deg6.045
r_scangle_other5.632
r_long_range_B_refined5.355
r_long_range_B_other5.315
r_scbond_other5.222
r_scbond_it5.218
r_mcangle_other4.427
r_mcangle_it4.416
r_mcbond_it3.871
r_mcbond_other3.83
r_angle_refined_deg2.736
r_angle_other_deg1.702
r_chiral_restr0.2
r_bond_refined_d0.033
r_gen_planes_refined0.013
r_gen_planes_other0.01
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 Atoms6424
Nucleic Acid Atoms
Solvent Atoms523
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
MOLREPphasing
Aimlessdata scaling