4R7P
Human UDP-glucose pyrophosphorylase isoform 1 in complex with UDP-glucose
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 281.15 | The protein sample contained 10.3 mg/ml of hUGP, 50 mM HEPES pH 7.5, 5 mM MgCl2, 1 mM EDTA, 20% (w/v) sucrose and 4 mM UDP-Glc. 1 l of the hUGP UDP-Glc complex was mixed 1:1 with the reservoir solution containing 100 mM sodium acetate buffer pH 4.8, 520 mM zinc acetate, 6% (w/v) aminocaproic acid and 75 mM ammonium sulfate. , VAPOR DIFFUSION, SITTING DROP, temperature 281.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.68 | 66.62 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 138.97 | α = 90 |
b = 138.97 | β = 90 |
c = 311.62 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 | ADSC QUANTUM 210 | 2011-04-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | ESRF | ID14-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 3.3 | 47.623 | 99.7 | 12.3 | 58213 | 2 | 96.27 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 3.35 | 47.62 | 1.34 | 49306 | 50946 | 2580 | 99.9 | 0.202 | 0.199 | 0.247 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.348 |
f_angle_d | 1.101 |
f_chiral_restr | 0.042 |
f_bond_d | 0.008 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15292 |
Nucleic Acid Atoms | |
Solvent Atoms | 117 |
Heterogen Atoms | 182 |
Software
Software | |
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Software Name | Purpose |
MxCuBE | data collection |
AMoRE | phasing |
PHENIX | refinement |
XDS | data reduction |
SADABS | data scaling |