4G3S

Crystal structure of GlmU from Mycobacterium tuberculosis in complex with uridine-diphosphate-n-acetylglucosamine and pyrophosphate Snapshot 2


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.58% PEG 8000, 150MM NACL, 5% GLYCEROL, 1,3-BUTANEDIOL,AMPPNP, MGCL2,0.1M HEPES, COCL2, DTT, pH 7.5, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.9858.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.58α = 90
b = 76.58β = 90
c = 276.97γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMIRRORS2009-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

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
12.0419.9499.20.06722.3538438-335.49
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)
12.042.0994.10.6043.24

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 REPLACEMENTTHROUGHOUT3DJ42.0419.9438392100799.30.1810.180.23RANDOM30.9
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.434
r_dihedral_angle_4_deg22.318
r_dihedral_angle_3_deg15.513
r_dihedral_angle_1_deg6.694
r_scangle_it5.674
r_scbond_it3.632
r_mcangle_it2.191
r_angle_refined_deg2.177
r_mcbond_it1.297
r_chiral_restr0.256
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.434
r_dihedral_angle_4_deg22.318
r_dihedral_angle_3_deg15.513
r_dihedral_angle_1_deg6.694
r_scangle_it5.674
r_scbond_it3.632
r_mcangle_it2.191
r_angle_refined_deg2.177
r_mcbond_it1.297
r_chiral_restr0.256
r_bond_refined_d0.027
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 Atoms3374
Nucleic Acid Atoms
Solvent Atoms371
Heterogen Atoms71

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling