5TCJ

Crystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate and BRD4592-bound form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5TCF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82898% tacsimate pH 8.0, 20% PEG3350, 10 mM BaCl2, 1 mM BRD4592, soaked with 100 mM CsCl and 50 mM L-Ser, cryo 16% ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
3.160.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.092α = 90
b = 159.875β = 90
c = 165.331γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2015-11-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97934APS19-ID

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
12.43099.90.13812.966.3138958-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4499.90.6491.695.8

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5TCF2.430136019271299.50.180820.180240.21074RANDOM41.368
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]
0.921.48-2.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.937
r_dihedral_angle_4_deg16.29
r_dihedral_angle_3_deg12.61
r_dihedral_angle_1_deg5.795
r_long_range_B_refined3.108
r_long_range_B_other3.107
r_angle_refined_deg1.291
r_scangle_other1.118
r_mcangle_it0.973
r_mcangle_other0.973
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.937
r_dihedral_angle_4_deg16.29
r_dihedral_angle_3_deg12.61
r_dihedral_angle_1_deg5.795
r_long_range_B_refined3.108
r_long_range_B_other3.107
r_angle_refined_deg1.291
r_scangle_other1.118
r_mcangle_it0.973
r_mcangle_other0.973
r_angle_other_deg0.933
r_scbond_it0.658
r_scbond_other0.65
r_mcbond_it0.552
r_mcbond_other0.552
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms19082
Nucleic Acid Atoms
Solvent Atoms720
Heterogen Atoms271

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling