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Crystal structure of the urea channel from the human gastric pathogen Helicobacter pylori
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.3 285 Drop: 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 coefficient Solvent content 4.1 69.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.904 α = 90 b = 122.904 β = 90 c = 141.348 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2011-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97911 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.256 92.746 98.8 0.05 21.2 6.2 17274 17263 2 1.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.256 3.43 97.9 1.108 1.6 6.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 3.26 39.35 17190 16314 872 98.18 0.24233 0.23929 0.2442 0.29949 0.3185 RANDOM 164.174
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 -0.63 1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.296 r_dihedral_angle_4_deg 19.295 r_dihedral_angle_3_deg 18.637 r_rigid_bond_restr 11.159 r_dihedral_angle_1_deg 7.742 r_angle_refined_deg 1.468 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.296 r_dihedral_angle_4_deg 19.295 r_dihedral_angle_3_deg 18.637 r_rigid_bond_restr 11.159 r_dihedral_angle_1_deg 7.742 r_angle_refined_deg 1.468 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 Atoms Number Protein Atoms 4284 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 198
Software Software Software Name Purpose ADSC data collection SHARP phasing REFMAC refinement XDS data reduction SCALA data scaling