3COZ

Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 2.0 Ang resolution- in complex with sulphonamide inhibitor 4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3COVPDB entry 3COV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293final soak solution: 12% PEG3000, 0.1 M imidazole, 4% ethanol, 10% glycerol, 6 mM of inhibitor 4, 3% v/v DMSO, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2244.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.6α = 90
b = 71.23β = 99.56
c = 82.02γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-02-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.979ESRFID29

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
125099.90.0990.0998.94.437805374272.523
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)
122.051000.4790.4794.32492

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 3COV247.953555735532187299.930.170130.170130.167640.21826RANDOM32.077
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_deg38.345
r_dihedral_angle_3_deg14.004
r_dihedral_angle_4_deg12.695
r_dihedral_angle_1_deg5.775
r_scangle_it5.41
r_mcangle_it3.926
r_scbond_it3.762
r_mcbond_it3.028
r_angle_refined_deg1.391
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.345
r_dihedral_angle_3_deg14.004
r_dihedral_angle_4_deg12.695
r_dihedral_angle_1_deg5.775
r_scangle_it5.41
r_mcangle_it3.926
r_scbond_it3.762
r_mcbond_it3.028
r_angle_refined_deg1.391
r_nbtor_refined0.306
r_symmetry_vdw_refined0.299
r_nbd_refined0.207
r_xyhbond_nbd_refined0.135
r_symmetry_hbond_refined0.106
r_chiral_restr0.089
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4174
Nucleic Acid Atoms
Solvent Atoms361
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing