3QJA

Crystal Structure of the Mycobacterium tuberculosis Indole-3-glycerol phosphate synthase (TrpC) in apo form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VC4PDB entry 1VC4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.52980.1M Sodium acetate trihydrate, 2.0M Ammonium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0540.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.069α = 90
b = 53.505β = 90
c = 87.826γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDmirrors2009-06-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.97933APS23-ID-D

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
11.295099.90.0670.06715.613.8590345903412.6
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)
11.291.311000.4240.4249.5412.82905

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 1VC41.2933.455878658786298099.750.16410.16410.16320.1809RANDOM16.1591
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]
0.02-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.697
r_dihedral_angle_4_deg15.172
r_dihedral_angle_3_deg11.13
r_dihedral_angle_1_deg4.835
r_sphericity_free3.079
r_scangle_it2.709
r_scbond_it1.8
r_rigid_bond_restr1.729
r_sphericity_bonded1.619
r_mcangle_it1.225
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.697
r_dihedral_angle_4_deg15.172
r_dihedral_angle_3_deg11.13
r_dihedral_angle_1_deg4.835
r_sphericity_free3.079
r_scangle_it2.709
r_scbond_it1.8
r_rigid_bond_restr1.729
r_sphericity_bonded1.619
r_mcangle_it1.225
r_angle_refined_deg1.097
r_angle_other_deg0.858
r_mcbond_it0.764
r_mcbond_other0.268
r_nbd_refined0.218
r_symmetry_vdw_other0.205
r_nbd_other0.195
r_symmetry_vdw_refined0.17
r_nbtor_refined0.164
r_symmetry_hbond_refined0.126
r_xyhbond_nbd_refined0.103
r_nbtor_other0.086
r_chiral_restr0.057
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1806
Nucleic Acid Atoms
Solvent Atoms285
Heterogen Atoms5

Software

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