2HY7

Crystal Structure of GumK, a beta-glucuronosyltransferase from Xanthomonas campestris


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.22930.1 M Tris-HCl, 35% (w/v) PEG 3350, 0.2 M Li2SO4, 0.1 M CsCl, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 8.20
Crystal Properties
Matthews coefficientSolvent content
4.2458.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.629α = 90
b = 123.629β = 90
c = 174.307γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210BEAM FOCUSED BY A TOROIDAL MIRROR2006-04-27MSINGLE WAVELENGTH
21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12CNSLSX12C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.9107.2111000.0690.0699.914.162401
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.921000.3440.3442.212.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT1.9107.21623676236331591000.1820.1810.204RANDOM18.6
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]
0.270.130.27-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.711
r_dihedral_angle_4_deg16.438
r_dihedral_angle_3_deg13.046
r_dihedral_angle_1_deg5.444
r_scangle_it3.491
r_scbond_it2.218
r_mcangle_it1.472
r_angle_refined_deg1.277
r_mcbond_it0.919
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.711
r_dihedral_angle_4_deg16.438
r_dihedral_angle_3_deg13.046
r_dihedral_angle_1_deg5.444
r_scangle_it3.491
r_scbond_it2.218
r_mcangle_it1.472
r_angle_refined_deg1.277
r_mcbond_it0.919
r_nbtor_refined0.31
r_symmetry_hbond_refined0.228
r_symmetry_vdw_refined0.224
r_nbd_refined0.213
r_xyhbond_nbd_refined0.179
r_chiral_restr0.089
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2963
Nucleic Acid Atoms
Solvent Atoms462
Heterogen Atoms

Software

Software
Software NamePurpose
SCALAdata scaling
SHARPphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction