3SPT

Crystal structure of GlmU from Mycobacterium tuberculosis in complex with ACETYL COENZYME A and URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DJ4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1sitting drop8.52910.1M Tris-Cl, pH-8.5, 2% Tacsimate, 18% PEG 3350, sitting drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
4.0269.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.194α = 90
b = 110.194β = 90
c = 361.295γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARCCD 225mirrors2011-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97625ESRFBM14

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
12.3319.80899.80.05424.8836542-342.057
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.332.3998.30.3590.3875.05

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 REPLACEMENTTHROUGHOUT3DJ42.3319.6835443100199.850.192910.192050.22359RANDOM31.524
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]
0.0001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.4
r_dihedral_angle_4_deg22.17
r_dihedral_angle_3_deg17.29
r_dihedral_angle_1_deg7.186
r_scangle_it6.09
r_scbond_it3.798
r_angle_refined_deg2.353
r_mcangle_it2.173
r_mcbond_it1.189
r_chiral_restr0.246
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.4
r_dihedral_angle_4_deg22.17
r_dihedral_angle_3_deg17.29
r_dihedral_angle_1_deg7.186
r_scangle_it6.09
r_scbond_it3.798
r_angle_refined_deg2.353
r_mcangle_it2.173
r_mcbond_it1.189
r_chiral_restr0.246
r_bond_refined_d0.026
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3471
Nucleic Acid Atoms
Solvent Atoms212
Heterogen Atoms93

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction