3UX4

Crystal structure of the urea channel from the human gastric pathogen Helicobacter pylori


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.3285Drop: 1.57 mg/mL UreI protein, 0.04 M NaCl, 1 mM TlCl, 0.01 M CaCl2, 7% PEG400, 0.05% decylmaltoside, 2.25% octylglucoside, 0.8 mg/mL E. coli polar lipids, 0.035 M MES, pH5.3, reservoir: 20% PEG400, 0.1 M MES, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties
Matthews coefficientSolvent content
4.169.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.904α = 90
b = 122.904β = 90
c = 141.348γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152011-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97911APS24-ID-C

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
13.25692.74698.80.0521.26.2172741726321.6
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)
13.2563.4397.91.1081.66.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT3.2639.35171901631487298.180.242330.239290.29949RANDOM164.174
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]
-0.63-0.631.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.296
r_dihedral_angle_4_deg19.295
r_dihedral_angle_3_deg18.637
r_rigid_bond_restr11.159
r_dihedral_angle_1_deg7.742
r_angle_refined_deg1.468
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.296
r_dihedral_angle_4_deg19.295
r_dihedral_angle_3_deg18.637
r_rigid_bond_restr11.159
r_dihedral_angle_1_deg7.742
r_angle_refined_deg1.468
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4284
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms198

Software

Software
Software NamePurpose
ADSCdata collection
SHARPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling