5C4E

Crystal structure of GTB + UDP-Glc + H-antigen acceptor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LZ0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP277Grown in 1% polyethylene glycol (PEG) 4000, 4.5-5% 2-methyl-2,4-pentanediol (MPD), 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM N-[-acetamido]-2-iminodiacetic acid (ADA), 30 mM sodium acetate, 5 mM manganese chloride. Grown 5-10 days.
Crystal Properties
Matthews coefficientSolvent content
2.346.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.64α = 90
b = 149.67β = 90
c = 79.46γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113IMAGE PLATERIGAKU RAXIS IV++2007-10-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.5574.8398.50.04615.64.245267
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)
11.551.6199.70.2733.73.494512

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 REPLACEMENTTHROUGHOUT1LZ01.5574.8342973228598.430.17440.17320.1979RANDOM20.834
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]
-0.750.120.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.529
r_dihedral_angle_4_deg17.963
r_dihedral_angle_3_deg12.348
r_dihedral_angle_1_deg7.368
r_mcangle_it1.964
r_angle_refined_deg1.612
r_mcbond_it1.267
r_mcbond_other1.264
r_angle_other_deg1.025
r_chiral_restr0.102
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.529
r_dihedral_angle_4_deg17.963
r_dihedral_angle_3_deg12.348
r_dihedral_angle_1_deg7.368
r_mcangle_it1.964
r_angle_refined_deg1.612
r_mcbond_it1.267
r_mcbond_other1.264
r_angle_other_deg1.025
r_chiral_restr0.102
r_bond_refined_d0.011
r_bond_other_d0.008
r_gen_planes_refined0.008
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2360
Nucleic Acid Atoms
Solvent Atoms275
Heterogen Atoms61

Software

Software
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Cootmodel building
PHASERphasing
CrystalCleardata reduction