3IMG

Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 1.8 Ang resolution in a ternary complex with fragment compounds 5-methoxyindole and 1-benzofuran-2-carboxylic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829311-14% w/v PEG3000, 100-150 mM lithium sulfate, 100 mM imidazole, pH 8.0, 2-4% v/v ethanol, 10% v/v glycerol and 20 mM magnesium chloride., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2144.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.48α = 90
b = 71.22β = 99.4
c = 81.8γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2008-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9788ESRFID29

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
11.85099.70.0610.06116.64.1509865081629.5
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)
11.81.9199.40.5290.5292.764.18124

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 3COV1.838.494841048270254399.710.169780.169780.167730.20909RANDOM27.439
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_deg37.147
r_dihedral_angle_4_deg15.113
r_dihedral_angle_3_deg13.223
r_dihedral_angle_1_deg5.67
r_scangle_it5.406
r_mcangle_it3.728
r_scbond_it3.55
r_mcbond_it2.815
r_angle_refined_deg1.401
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.147
r_dihedral_angle_4_deg15.113
r_dihedral_angle_3_deg13.223
r_dihedral_angle_1_deg5.67
r_scangle_it5.406
r_mcangle_it3.728
r_scbond_it3.55
r_mcbond_it2.815
r_angle_refined_deg1.401
r_nbtor_refined0.307
r_nbd_refined0.209
r_symmetry_vdw_refined0.169
r_xyhbond_nbd_refined0.15
r_symmetry_hbond_refined0.096
r_chiral_restr0.094
r_bond_refined_d0.014
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4126
Nucleic Acid Atoms
Solvent Atoms382
Heterogen Atoms73

Software

Software
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement