1Q51

Crystal Structure of Mycobacterium tuberculosis MenB in Complex with Acetoacetyl-Coenzyme A, a Key Enzyme in Vitamin K2 Biosynthesis


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5295dioxane, ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.1342.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.401α = 90
b = 139.389β = 97.31
c = 142.041γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-11-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X26C1.1NSLSX26C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.350146353

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT1DUB2.350146353777799.620.203690.203690.201710.24106RANDOM34.919
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]
4.240.1-1.59-2.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.394
r_scangle_it2.895
r_scbond_it1.831
r_angle_refined_deg1.495
r_mcangle_it1.231
r_mcbond_it0.639
r_symmetry_vdw_refined0.22
r_nbd_refined0.204
r_xyhbond_nbd_refined0.134
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.394
r_scangle_it2.895
r_scbond_it1.831
r_angle_refined_deg1.495
r_mcangle_it1.231
r_mcbond_it0.639
r_symmetry_vdw_refined0.22
r_nbd_refined0.204
r_xyhbond_nbd_refined0.134
r_chiral_restr0.107
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms25697
Nucleic Acid Atoms
Solvent Atoms422
Heterogen Atoms648

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing