3JT1

Legionella pneumophila glucosyltransferase Lgt1, UDP-bound form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3JSZPDB ENTRY 3JSZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15293.151ul protein (4mg/ml) was mixed with 1ul of reservoir solution containing 23% PEG3350, 0.06M ammonium acetat, 0.1M sodium acetate buffer, pH5.0, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.5251.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.571α = 90
b = 122.571β = 90
c = 103.982γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayPIXELPSI PILATUS 6M2009-08-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.000SLSX06SA

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
12.331.899.80.1028.45.12654122
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)
12.32.499.80.6572.15.119778

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3JSZ2.331.7625175134399.910.189030.185160.26158RANDOM38.62
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]
-2.84-1.42-2.844.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.848
r_dihedral_angle_4_deg26.934
r_dihedral_angle_3_deg17.509
r_dihedral_angle_1_deg6.726
r_scangle_it4.599
r_scbond_it2.823
r_angle_refined_deg1.949
r_mcangle_it1.914
r_mcbond_it1.042
r_angle_other_deg1.041
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.848
r_dihedral_angle_4_deg26.934
r_dihedral_angle_3_deg17.509
r_dihedral_angle_1_deg6.726
r_scangle_it4.599
r_scbond_it2.823
r_angle_refined_deg1.949
r_mcangle_it1.914
r_mcbond_it1.042
r_angle_other_deg1.041
r_mcbond_other0.232
r_chiral_restr0.103
r_bond_refined_d0.023
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms4023
Nucleic Acid Atoms
Solvent Atoms182
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement