3C4V

Structure of the retaining glycosyltransferase MshA:The first step in mycothiol biosynthesis. Organism: Corynebacterium glutamicum : Complex with UDP and 1L-INS-1-P.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3C4QPDB entry 3C4Q

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.5298Protein (40 mg/ml, 400 mM Ammonium sulfate, 10% glycerol, 0.5 mM EDTA, 1 mM BME, 10 mM UDPNAG) Precipitant (0.8 M sodium citrate pH 5.5 ) , Vapor diffusion under oil, temperature 298K, VAPOR DIFFUSION
Crystal Properties
Matthews coefficientSolvent content
4.1970.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 223.94α = 90
b = 223.94β = 90
c = 125.005γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 315Optics Meridionally-bent fused silica mirror with palladium and uncoated stripes2007-10-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X250.9778NSLSX25

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
12.68099.60.0560.056235.2485534855362
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)
2.62.741000.3090.30944.97040

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3C4Q2.679.184608946089246399.390.191220.191220.190050.21304RANDOM44.585
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]
-0.41-0.410.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.799
r_dihedral_angle_4_deg21.156
r_dihedral_angle_3_deg18.034
r_dihedral_angle_1_deg12.985
r_scangle_it2.661
r_scbond_it1.614
r_angle_refined_deg1.606
r_mcangle_it1.018
r_mcbond_it0.593
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.799
r_dihedral_angle_4_deg21.156
r_dihedral_angle_3_deg18.034
r_dihedral_angle_1_deg12.985
r_scangle_it2.661
r_scbond_it1.614
r_angle_refined_deg1.606
r_mcangle_it1.018
r_mcbond_it0.593
r_nbtor_refined0.308
r_symmetry_hbond_refined0.232
r_nbd_refined0.217
r_symmetry_vdw_refined0.188
r_xyhbond_nbd_refined0.131
r_chiral_restr0.11
r_bond_refined_d0.014
r_gen_planes_refined0.005
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 Atoms6051
Nucleic Acid Atoms
Solvent Atoms70
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
CBASSdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing