2ICY
Crystal Structure of a Putative UDP-glucose Pyrophosphorylase from Arabidopsis Thaliana with Bound UDP-glucose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1Z90 | pdb entry 1Z90 |
Crystallization
Crystalization Experiments | ||||
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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 UDP-glucose, vapor diffusion, hanging drop with micro-seeding, temperature 273K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 188.008 | α = 90 |
b = 59.712 | β = 100.32 |
c = 89.762 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR | 2005-10-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 0.97911 | 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 | 1.64 | 38.25 | 98.8 | 0.042 | 20.7 | 4.3 | 118994 | 118994 | 23 |
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 | 1.64 | 1.68 | 83.1 | 0.295 | 3.894 | 3.3 | 6594 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 1Z90 | 1.64 | 38.25 | 119685 | 118994 | 5964 | 99.4 | 0.183 | 0.223 | random | 25.74 |
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] | |
-1.04 | -0.6 | 2.32 | -1.27 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 24.8 |
c_angle_deg | 2 |
c_improper_angle_d | 1.3 |
c_bond_d | 0.019 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7152 |
Nucleic Acid Atoms | |
Solvent Atoms | 848 |
Heterogen Atoms | 76 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |
CNS | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |