3MQH

crystal structure of the 3-N-acetyl transferase WlbB from Bordetella petrii in complex with CoA and UDP-3-amino-2-acetamido-2,3-dideoxy glucuronic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MQGPDB ENTRY 3MQG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829516-20% PEG3400, 210 mM tetramethylammonium chloride, 100 mM HEPPS, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.6453.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.466α = 90
b = 107.891β = 102.55
c = 91.269γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2009-10-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97921APS19-BM

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
11.4350900.0770.07728.32.9213775213775
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)
1.431.4876.10.1250.1256.62.117966

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 3MQG1.43302137752030891068689.90.1760.175780.174170.20645RANDOM13.093
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]
-0.360.52-0.741.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.894
r_dihedral_angle_4_deg19.436
r_dihedral_angle_3_deg12.373
r_dihedral_angle_1_deg6.547
r_scangle_it4.989
r_scbond_it3.222
r_angle_refined_deg2.124
r_mcangle_it1.975
r_mcbond_it1.291
r_chiral_restr0.145
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.894
r_dihedral_angle_4_deg19.436
r_dihedral_angle_3_deg12.373
r_dihedral_angle_1_deg6.547
r_scangle_it4.989
r_scbond_it3.222
r_angle_refined_deg2.124
r_mcangle_it1.975
r_mcbond_it1.291
r_chiral_restr0.145
r_bond_refined_d0.012
r_gen_planes_refined0.007
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 Atoms8690
Nucleic Acid Atoms
Solvent Atoms1698
Heterogen Atoms612

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling