3UX4
Crystal structure of the urea channel from the human gastric pathogen Helicobacter pylori
X-RAY DIFFRACTION
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | THROUGHOUT | 3.26 | 39.35 | 17190 | 16314 | 872 | 98.18 | 0.24233 | 0.23929 | 0.29949 | 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 |
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 |