3T44 | pdb_00003t44

Crystal structure of Mycobacterium tuberculosis Indole Glycerol Phosphate Synthase (IGPS) in complex with indole glycerol phosphate (IGP) amd anthranilate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IGSPDB entry 1IGS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.52980.1M Sodium acetate trihydrate, 2.0 ammonium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9235.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.553α = 90
b = 53.222β = 90
c = 86.855γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2009-08-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9771APS19-ID

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
11.65099.80.1120.112107.1287842878414.5
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)
11.61.631000.4540.4545.487.21390

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1IGS1.626.6128717146498.680.15050.14820.160.1950.21RANDOM20.7094
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]
0.1-0.04-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.822
r_dihedral_angle_4_deg16.761
r_dihedral_angle_3_deg11.33
r_dihedral_angle_1_deg4.859
r_scangle_it3.607
r_scbond_it2.519
r_mcangle_it1.516
r_angle_refined_deg1.287
r_mcbond_it1.026
r_angle_other_deg0.889
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.822
r_dihedral_angle_4_deg16.761
r_dihedral_angle_3_deg11.33
r_dihedral_angle_1_deg4.859
r_scangle_it3.607
r_scbond_it2.519
r_mcangle_it1.516
r_angle_refined_deg1.287
r_mcbond_it1.026
r_angle_other_deg0.889
r_mcbond_other0.406
r_symmetry_vdw_other0.241
r_nbd_refined0.216
r_nbd_other0.207
r_nbtor_refined0.171
r_symmetry_vdw_refined0.155
r_symmetry_hbond_refined0.154
r_xyhbond_nbd_refined0.144
r_nbtor_other0.095
r_chiral_restr0.071
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1849
Nucleic Acid Atoms
Solvent Atoms292
Heterogen Atoms29

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection