3IMC

Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 1.6 Ang resolution in complex with fragment compound 5-methoxyindole, sulfate and glycerol


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
2.1943.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.234α = 90
b = 70.9β = 99.22
c = 81.852γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-09-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.973ESRFID29

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
11.650.198.70.0740.07412.43.5713447041716.7
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)
11.61.6496.60.320.3234576

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 3COV1.647.626781166631354798.260.169680.169680.167820.20369RANDOM19.461
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_deg36.793
r_dihedral_angle_4_deg15.668
r_dihedral_angle_3_deg12.548
r_dihedral_angle_1_deg5.366
r_scangle_it4.408
r_scbond_it2.881
r_mcangle_it2.865
r_mcbond_it2.081
r_angle_refined_deg1.263
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.793
r_dihedral_angle_4_deg15.668
r_dihedral_angle_3_deg12.548
r_dihedral_angle_1_deg5.366
r_scangle_it4.408
r_scbond_it2.881
r_mcangle_it2.865
r_mcbond_it2.081
r_angle_refined_deg1.263
r_nbtor_refined0.308
r_nbd_refined0.202
r_symmetry_vdw_refined0.17
r_xyhbond_nbd_refined0.134
r_symmetry_hbond_refined0.105
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4133
Nucleic Acid Atoms
Solvent Atoms593
Heterogen Atoms69

Software

Software
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling