3COY

Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 2.05 Ang resolution- in complex with sulphonamide inhibitor 3


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 3, 3% v/v DMSO, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2144.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.49α = 90
b = 71.2β = 99.8
c = 81.85γ = 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
12.0550.598.30.070.079.34.635124345272.531.1
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)
12.052.197.10.4660.4664.32307

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 3COV2.0344.593364032796173097.490.169040.169040.166250.22106RANDOM38.096
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]
0.01-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.599
r_dihedral_angle_4_deg19.348
r_dihedral_angle_3_deg16.026
r_dihedral_angle_1_deg5.664
r_scangle_it4.91
r_mcangle_it3.807
r_scbond_it3.508
r_mcbond_it2.911
r_angle_refined_deg1.394
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.599
r_dihedral_angle_4_deg19.348
r_dihedral_angle_3_deg16.026
r_dihedral_angle_1_deg5.664
r_scangle_it4.91
r_mcangle_it3.807
r_scbond_it3.508
r_mcbond_it2.911
r_angle_refined_deg1.394
r_nbtor_refined0.305
r_nbd_refined0.207
r_symmetry_vdw_refined0.18
r_xyhbond_nbd_refined0.14
r_symmetry_hbond_refined0.126
r_chiral_restr0.091
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4133
Nucleic Acid Atoms
Solvent Atoms369
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing