3UB6

Periplasmic portion of the Helicobacter pylori chemoreceptor TlpB with urea bound


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52770.1 M PIPES pH 6.5, 22% PEG 3350, 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.7266.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.608α = 90
b = 81.881β = 90
c = 94.534γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rRh/Pt coated2008-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.977ALS5.0.3

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
11.385099.40.07113.38.6127039126318-3
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)
11.381.498.30.496.66208

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSIRASTHROUGHOUT1.3847.27126197126197632099.410.12450.12450.12330.1464RANDOM18.2775
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]
-0.09-0.060.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.718
r_sphericity_free19.163
r_dihedral_angle_3_deg9.654
r_sphericity_bonded8.378
r_scangle_it7.89
r_dihedral_angle_4_deg6.576
r_scbond_it5.962
r_dihedral_angle_1_deg4.605
r_mcangle_it3.783
r_rigid_bond_restr3.062
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.718
r_sphericity_free19.163
r_dihedral_angle_3_deg9.654
r_sphericity_bonded8.378
r_scangle_it7.89
r_dihedral_angle_4_deg6.576
r_scbond_it5.962
r_dihedral_angle_1_deg4.605
r_mcangle_it3.783
r_rigid_bond_restr3.062
r_mcbond_it2.755
r_mcbond_other1.515
r_angle_refined_deg1.484
r_angle_other_deg0.909
r_chiral_restr0.101
r_bond_refined_d0.017
r_gen_planes_refined0.015
r_gen_planes_other0.003
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2550
Nucleic Acid Atoms
Solvent Atoms575
Heterogen Atoms84

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
SHELXSphasing