3RU6
1.8 Angstrom resolution crystal structure of orotidine 5'-phosphate decarboxylase (pyrF) from Campylobacter jejuni subsp. jejuni NCTC 11168
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 295 | Protein: 7.3 mg/mL in 10 mM Tris/HCl pH 8.3, 0.25 M NaCl, 5 mM BME. Crystallization condition: The PACT suite (F3 (63): 0.2 M Sodium iodide, 0.1 M Bis Tris propane pH 6.5, 20 % w/v PEG3350). Mixed 1:1 v/v , VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.35 | 47.65 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.598 | α = 90 |
b = 108.308 | β = 95.73 |
c = 97.707 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | MARMOSAIC 300 mm CCD | Be Lenses/Diamond Laue Mono | 2011-04-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.8 | 30 | 98.4 | 0.05 | 18.41 | 2.6 | 84340 | 84340 | -3 | 26.2 |
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 | 1.8 | 1.83 | 97.5 | 0.564 | 1.86 | 2.5 | 4147 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | balbes | 1.8 | 29.12 | 79775 | 79775 | 4208 | 98.41 | 0.17005 | 0.16837 | 0.20267 | RANDOM | 32.773 |
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] | |
-1.48 | -0.69 | 0.55 | 0.79 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.559 |
r_dihedral_angle_4_deg | 7.603 |
r_dihedral_angle_3_deg | 7.077 |
r_scangle_it | 3.499 |
r_scbond_it | 2.087 |
r_dihedral_angle_1_deg | 1.906 |
r_angle_refined_deg | 1.503 |
r_mcangle_it | 1.202 |
r_angle_other_deg | 0.862 |
r_mcbond_it | 0.631 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6993 |
Nucleic Acid Atoms | |
Solvent Atoms | 549 |
Heterogen Atoms | 30 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
BALBES | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |