1Z90

X-ray structure of gene product from arabidopsis thaliana at3g03250, a putative UDP-glucose pyrophosphorylase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.52931 mg/ml protein, 30% PEG2K, 0.100M MES/ACETATE, 5% DMSO, vapor diffusion, hanging drop, pH 5.5, temperature 293K
25.52931 mg/ml protein, 30% PEG2K, 0.100M MES/ACETATE, 5% DMSO, vapor diffusion, hanging drop, pH 5.5, temperature 293K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 188.68α = 90
b = 58.863β = 100.4
c = 89.862γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDHORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR2005-03-13MSINGLE WAVELENGTH
21x-ray100CCDMARMOSAIC 300 mm CCDHORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR2005-03-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BMAPS22-BM
2SYNCHROTRONAPS BEAMLINE 22-IDAPS22-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
1,21.86337.365980.06617.377779505
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)
1.861.989.50.3953.2245.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.865075518398697.70.203190.2010.249RANDOM31.48
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]
-0.79-1.22-0.250.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.434
r_dihedral_angle_4_deg17.45
r_dihedral_angle_3_deg16.783
r_angle_other_deg16.409
r_scangle_it6.843
r_dihedral_angle_1_deg6.359
r_scbond_it4.837
r_mcangle_it2.948
r_mcbond_it1.73
r_angle_refined_deg1.607
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.434
r_dihedral_angle_4_deg17.45
r_dihedral_angle_3_deg16.783
r_angle_other_deg16.409
r_scangle_it6.843
r_dihedral_angle_1_deg6.359
r_scbond_it4.837
r_mcangle_it2.948
r_mcbond_it1.73
r_angle_refined_deg1.607
r_mcbond_other0.411
r_nbtor_refined0.312
r_nbtor_other0.288
r_nbd_refined0.221
r_symmetry_hbond_refined0.214
r_symmetry_vdw_refined0.198
r_nbd_other0.168
r_xyhbond_nbd_refined0.162
r_chiral_restr0.11
r_bond_other_d0.097
r_gen_planes_other0.033
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7122
Nucleic Acid Atoms
Solvent Atoms421
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RESOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing