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)
TypeSourceAccession CodeDetails
experimental modelPDB 1Z90 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1vapor diffusion, hanging drop with micro-seeding273Protein 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
Length ( Å )Angle ( ˚ )
a = 187.683α = 90
b = 59.679β = 100.38
c = 89.813γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER PROTEUM-RMONTEL OPTICS2006-05-02SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.8570.48199.40.035323.914.383235
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.851.91000.31153.195.096377

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1Z901.8570.48183222415899.3710.1950.1920.239RANDOM11.405
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]
-0.363-0.235-0.3980.676
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.005
r_dihedral_angle_3_deg14.536
r_dihedral_angle_4_deg13.597
r_dihedral_angle_1_deg5.963
r_scangle_it3.454
r_scbond_it2.253
r_angle_refined_deg1.902
r_mcangle_it1.298
r_mcbond_it0.868
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.005
r_dihedral_angle_3_deg14.536
r_dihedral_angle_4_deg13.597
r_dihedral_angle_1_deg5.963
r_scangle_it3.454
r_scbond_it2.253
r_angle_refined_deg1.902
r_mcangle_it1.298
r_mcbond_it0.868
r_nbtor_refined0.308
r_nbd_refined0.208
r_symmetry_vdw_refined0.191
r_xyhbond_nbd_refined0.146
r_symmetry_hbond_refined0.134
r_chiral_restr0.106
r_bond_refined_d0.016
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7132
Nucleic Acid Atoms
Solvent Atoms871
Heterogen Atoms62

Software

Software
Software NamePurpose
SAINTdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SAINTdata reduction
SADABSdata scaling