5TCH | pdb_00005tch

Crystal structure of tryptophan synthase from M. tuberculosis - ligand-free form, TrpA-G66V mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82898% tacsimate pH 8.0, 20% PEG3350, cryo 20% ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
3.0759.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.321α = 90
b = 158.813β = 90
c = 166.218γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2015-12-01MSINGLE 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
12.35301000.124177.1148100-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.3999.90.8950.7072.056

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-Work (Depositor)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT2.3530145047288399.690.175650.175050.20571RANDOM42.69
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]
-0.651.89-1.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.099
r_dihedral_angle_4_deg16.621
r_dihedral_angle_3_deg13.259
r_dihedral_angle_1_deg6.027
r_long_range_B_refined3.999
r_long_range_B_other3.998
r_scangle_other1.804
r_mcangle_it1.46
r_mcangle_other1.46
r_angle_refined_deg1.422
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.099
r_dihedral_angle_4_deg16.621
r_dihedral_angle_3_deg13.259
r_dihedral_angle_1_deg6.027
r_long_range_B_refined3.999
r_long_range_B_other3.998
r_scangle_other1.804
r_mcangle_it1.46
r_mcangle_other1.46
r_angle_refined_deg1.422
r_scbond_it1.078
r_scbond_other1.066
r_angle_other_deg0.968
r_mcbond_other0.847
r_mcbond_it0.846
r_chiral_restr0.077
r_bond_refined_d0.011
r_gen_planes_refined0.006
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 Atoms19214
Nucleic Acid Atoms
Solvent Atoms795
Heterogen Atoms116

Software

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