2V25

Structure of the Campylobacter jejuni antigen Peb1A, an aspartate and glutamate receptor with bound aspartate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XT8PDB ENTRY 1XT8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
160.01 M ZINC CHLORIDE, 0.1 M HEPES PH 7 AND 20 % W/V PEG 6000
Crystal Properties
Matthews coefficientSolvent content
239

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.272α = 90
b = 75.868β = 103.31
c = 61.708γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2005-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.54099.30.1413.55.1753462
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5585.90.3321.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1XT81.4960.0870979375996.70.1650.1630.185RANDOM9.77
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]
0.790.11-0.38-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.34
r_dihedral_angle_4_deg18.279
r_dihedral_angle_3_deg11.175
r_dihedral_angle_1_deg7.448
r_scangle_it2.289
r_scbond_it1.683
r_angle_refined_deg1.272
r_mcangle_it1.243
r_mcbond_it0.923
r_angle_other_deg0.824
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.34
r_dihedral_angle_4_deg18.279
r_dihedral_angle_3_deg11.175
r_dihedral_angle_1_deg7.448
r_scangle_it2.289
r_scbond_it1.683
r_angle_refined_deg1.272
r_mcangle_it1.243
r_mcbond_it0.923
r_angle_other_deg0.824
r_nbd_refined0.222
r_nbd_other0.185
r_nbtor_refined0.175
r_symmetry_vdw_other0.161
r_symmetry_hbond_refined0.161
r_symmetry_vdw_refined0.148
r_xyhbond_nbd_refined0.112
r_nbtor_other0.084
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3525
Nucleic Acid Atoms
Solvent Atoms532
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing