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)
TypeSourceAccession CodeDetails
experimental modelPDB 1Z90pdb entry 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 UDP-glucose, vapor diffusion, hanging drop with micro-seeding, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
2.3948.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 188.008α = 90
b = 59.712β = 100.32
c = 89.762γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDHORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR2005-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.97911APS22-ID

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
11.6438.2598.80.04220.74.311899411899423
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)
11.641.6883.10.2953.8943.36594

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1Z901.6438.25119685118994596499.40.1830.223random25.74
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]
-1.04-0.62.32-1.27
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.8
c_angle_deg2
c_improper_angle_d1.3
c_bond_d0.019
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7152
Nucleic Acid Atoms
Solvent Atoms848
Heterogen Atoms76

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction