3TJ9
Crystal structure of Helicobacter pylori UreE bound to Zn2+
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 4.0M sodium formate, 0.1M sodium cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.11 | 60.46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 109.343 | α = 90 |
b = 109.343 | β = 90 |
c = 280.343 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | RAYONIX MX-225 | 2010-05-15 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.2 | 1.2818, 1.2832, 1.2765 | BESSY | 14.2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.52 | 50 | 99.9 | 0.092 | 22.4 | 9.4 | 34454 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.52 | 2.56 | 98.2 | 0.43 | 3.4 | 6.9 | 1654 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | MAD | THROUGHOUT | 2.521 | 19.83 | 33219 | 1051 | 99.94 | 0.20389 | 0.20261 | 0.24484 | RANDOM | 39.727 |
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] | |
0.12 | 0.06 | 0.12 | -0.18 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.397 |
r_dihedral_angle_4_deg | 18.397 |
r_dihedral_angle_3_deg | 17.946 |
r_dihedral_angle_1_deg | 7.131 |
r_scangle_it | 5.821 |
r_scbond_it | 3.301 |
r_angle_refined_deg | 1.909 |
r_mcangle_it | 1.759 |
r_mcbond_it | 0.902 |
r_chiral_restr | 0.114 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4697 |
Nucleic Acid Atoms | |
Solvent Atoms | 187 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
MxCuBE | data collection |
Auto-Rickshaw | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |