1Z90
X-ray structure of gene product from arabidopsis thaliana at3g03250, a putative UDP-glucose pyrophosphorylase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5.5 | 293 | 1 mg/ml protein, 30% PEG2K, 0.100M MES/ACETATE, 5% DMSO, vapor diffusion, hanging drop, pH 5.5, temperature 293K | |
2 | 5.5 | 293 | 1 mg/ml protein, 30% PEG2K, 0.100M MES/ACETATE, 5% DMSO, vapor diffusion, hanging drop, pH 5.5, temperature 293K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 188.68 | α = 90 |
b = 58.863 | β = 100.4 |
c = 89.862 | 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 225 mm CCD | HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR | 2005-03-13 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR | 2005-03-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-BM | APS | 22-BM | |
2 | 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 | 1.863 | 37.365 | 98 | 0.066 | 17.377 | 7 | 79505 |
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) | |||||||||||
1.86 | 1.9 | 89.5 | 0.395 | 3.224 | 5.1 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.86 | 50 | 75518 | 3986 | 97.7 | 0.20319 | 0.201 | 0.249 | RANDOM | 31.48 |
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] | |
-0.79 | -1.22 | -0.25 | 0.6 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.434 |
r_dihedral_angle_4_deg | 17.45 |
r_dihedral_angle_3_deg | 16.783 |
r_angle_other_deg | 16.409 |
r_scangle_it | 6.843 |
r_dihedral_angle_1_deg | 6.359 |
r_scbond_it | 4.837 |
r_mcangle_it | 2.948 |
r_mcbond_it | 1.73 |
r_angle_refined_deg | 1.607 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7122 |
Nucleic Acid Atoms | |
Solvent Atoms | 421 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | phasing |
RESOLVE | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHENIX | phasing |