2XTZ
Crystal structure of the G alpha protein AtGPA1 from Arabidopsis thaliana
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 277 | CRYSTALS OF ATGPA1 WERE GROWN AT 4 DEGREES CELSIUS USING THE HANGING-DROP VAPOR-DIFFUSION METHOD. DROPS CONTAINED 1.5 UL OF PROTEIN SOLUTION (20 MG/ML ATGPA1 IN 25 MM TRIS-HCL, PH 7.4, 5% (V/V) GLYCEROL, 150 MM SODIUM CHLORIDE, 1 MM DTT, 500 UL GTP-GAMMA-S) AND WERE EQUILIBRATED AGAINST 1.5 UL OF 0.3 M MAGNESIUM SULFATE, 0.1 M SODIUM CACODYLATE, PH 6.0, 21% (W/V) PEG 8000. INITIALLY OBTAINED CRYSTALS WERE USED FOR MACROSEEDING. CRYSTALS REACHED THEIR FINAL ROD-SHAPE FORM WITHIN 14 DAYS AFTER MACROSEEDING AND WERE CRYOPROTECTED IN THE MOTHER LIQUOR WITH 8% (V/V) GLYCEROL. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 53.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.13 | α = 90 |
b = 119.347 | β = 90 |
c = 161.725 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | MARRESEARCH MX300 | CUSTOM | 2009-11-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | APS | 22-ID |
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 | 2.34 | 44.6 | 100 | 0.11 | 17.5 | 6 | 55808 | -3 | 52.9 |
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 | 2.34 | 2.36 | 100 | 0.84 | 1.9 | 5.8 |
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 1FQJ | 2.34 | 96.03 | 54216 | 1520 | 99.89 | 0.21247 | 0.2113 | 0.25378 | RANDOM | 44.512 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.03 | 1.37 | -1.4 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.609 |
r_dihedral_angle_4_deg | 19.857 |
r_dihedral_angle_3_deg | 15.294 |
r_dihedral_angle_1_deg | 5.256 |
r_scangle_it | 2.368 |
r_scbond_it | 1.473 |
r_angle_refined_deg | 1.249 |
r_mcangle_it | 0.802 |
r_mcbond_it | 0.407 |
r_nbtor_refined | 0.304 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7505 |
Nucleic Acid Atoms | |
Solvent Atoms | 249 |
Heterogen Atoms | 128 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |