3SGW
Crystal structure of ribose-5-phosphate isomerase B RpiB from Coccidioides immitis semi-covalently bound to malonic acid
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5 | 289 | protein at 66 mg/mL with 20 mM ribose-5-phosphate and 12 mM MnCl2. Reservoir: 25% PEG 1500 and 0.1 M MIB (malonic acid, imidazole, boric acid), with 25% ethylene glycol as cryo-protection reagent, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.99 | 38.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 77.46 | α = 90 |
b = 84.42 | β = 90 |
c = 96.17 | γ = 90 |
Symmetry | |
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Space Group | F 2 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 | RIGAKU SATURN 944+ | VariMax | 2011-06-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
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 | 1.7 | 50 | 94.5 | 0.044 | 34.74 | 9.6 | 17530 | 16561 | -3 | 20.011 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.7 | 1.74 | 80.2 | 0.256 | 6.62 | 5.3 | 1281 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 3SDW | 1.7 | 49.08 | 16509 | 832 | 94.19 | 0.1438 | 0.1421 | 0.1749 | RANDOM | 13.745 |
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] | |
-0.26 | 0.68 | -0.41 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.788 |
r_dihedral_angle_3_deg | 10.199 |
r_dihedral_angle_4_deg | 6.074 |
r_dihedral_angle_1_deg | 5.1 |
r_scangle_it | 3.535 |
r_scbond_it | 2.024 |
r_angle_refined_deg | 1.323 |
r_mcangle_it | 1.119 |
r_mcbond_it | 0.641 |
r_chiral_restr | 0.087 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1183 |
Nucleic Acid Atoms | |
Solvent Atoms | 168 |
Heterogen Atoms | 17 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
StructureStudio | data collection |
XDS | data reduction |