3ISJ

Crystal structure of pantothenate synthetase from Mycobacterium tuberculosis in complex with 5-methoxy-N-(methylsulfonyl)-1H-indole-2-carboxamide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829312-14% PEG 3000, 100-150 mM Li2SO4, 100-150 mM Imidazole, 2-4% Ethanol, 5-10% Glycerol, 20 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.346.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.24α = 90
b = 71.13β = 99.68
c = 81.71γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.93ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.240.260.10526779
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.250.586

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.240.2625424134096.270.174910.169910.26613RANDOM37.308
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]
0.82-1.071.75-2.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.817
r_dihedral_angle_4_deg17.141
r_dihedral_angle_3_deg17.135
r_dihedral_angle_1_deg7.609
r_scangle_it4.541
r_scbond_it3.057
r_mcangle_it2.021
r_angle_refined_deg2.017
r_mcbond_it1.236
r_symmetry_hbond_refined0.318
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.817
r_dihedral_angle_4_deg17.141
r_dihedral_angle_3_deg17.135
r_dihedral_angle_1_deg7.609
r_scangle_it4.541
r_scbond_it3.057
r_mcangle_it2.021
r_angle_refined_deg2.017
r_mcbond_it1.236
r_symmetry_hbond_refined0.318
r_nbtor_refined0.313
r_symmetry_vdw_refined0.285
r_nbd_refined0.232
r_xyhbond_nbd_refined0.222
r_chiral_restr0.132
r_bond_refined_d0.022
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4169
Nucleic Acid Atoms
Solvent Atoms400
Heterogen Atoms86

Software

Software
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling