2ICX
Crystal Structure of a Putative UDP-glucose Pyrophosphorylase from Arabidopsis Thaliana with Bound UTP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1Z90 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | vapor diffusion, hanging drop with micro-seeding | 273 | Protein solution (10 mg/ml protein, 0.050 M sodium chloride, 0.0003 M TCEP, 0.005 M Tris PH 8.0) mixed in a 1:1 ratio with Well solution ( 28 % PEG 2K, 5% DMSO, 0.10 M MES/Acetate pH 5.5), crystals soaked in well solution supplemented with 0.002 M UTP, vapor diffusion, hanging drop with micro-seeding, temperature 273K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 187.683 | α = 90 |
b = 59.679 | β = 100.38 |
c = 89.813 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | BRUKER PROTEUM-R | MONTEL OPTICS | 2006-05-02 | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.5418 |
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 | 1.85 | 70.481 | 99.4 | 0.0353 | 23.9 | 14.3 | 83235 |
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) | |||||||||||
1.85 | 1.9 | 100 | 0.3115 | 3.19 | 5.09 | 6377 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1Z90 | 1.85 | 70.481 | 83222 | 4158 | 99.371 | 0.195 | 0.192 | 0.239 | RANDOM | 11.405 |
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] | |
-0.363 | -0.235 | -0.398 | 0.676 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.005 |
r_dihedral_angle_3_deg | 14.536 |
r_dihedral_angle_4_deg | 13.597 |
r_dihedral_angle_1_deg | 5.963 |
r_scangle_it | 3.454 |
r_scbond_it | 2.253 |
r_angle_refined_deg | 1.902 |
r_mcangle_it | 1.298 |
r_mcbond_it | 0.868 |
r_nbtor_refined | 0.308 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7132 |
Nucleic Acid Atoms | |
Solvent Atoms | 871 |
Heterogen Atoms | 62 |
Software
Software | |
---|---|
Software Name | Purpose |
SAINT | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
SAINT | data reduction |
SADABS | data scaling |