9D3H | pdb_00009d3h

Thermotoga maritima threonylcarbamoyl adenylate synthase (TsaC2) in complex with N-carboxy-L-threonine, magnesium and pyrophosphate.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFoldAF-Q9WZV6-F1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.4294.15Reservoir solution: 500 ul 80 mM sodium cacodylate, pH 7.4, 0.15 M sodium acetate, 14.3% PEG8000, 20% glycerol Protein: 25 mg/mL TmTsaC2, 50 mM Tris, pH 7.5, 50 mM KCl, 1 mM DTT, 10 mM L-threonine, 10 mM ATP, 10 mM MgCl2, 30 mM sodium acetate; protein was preheated at 60 C for 30 mins drop is 1.5 ul reservoir + 1.5 ul sample.
Crystal Properties
Matthews coefficientSolvent content
3.968.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.039α = 90
b = 154.039β = 90
c = 87.241γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS EIGER X 9M2024-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X17B10.920105NSLSX17B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.27734.0999.10.3740.390.1080.37.712.854251
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.2772.3171003.6853.8361.060.419

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-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.2834.0951476272498.970.188730.187470.19130.212460.1859RANDOM47.005
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]
0.230.110.23-0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.787
r_dihedral_angle_4_deg21.551
r_dihedral_angle_3_deg17.684
r_dihedral_angle_1_deg7.248
r_long_range_B_refined4.848
r_long_range_B_other4.848
r_scangle_other2.405
r_mcangle_other1.761
r_mcangle_it1.76
r_angle_refined_deg1.563
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.787
r_dihedral_angle_4_deg21.551
r_dihedral_angle_3_deg17.684
r_dihedral_angle_1_deg7.248
r_long_range_B_refined4.848
r_long_range_B_other4.848
r_scangle_other2.405
r_mcangle_other1.761
r_mcangle_it1.76
r_angle_refined_deg1.563
r_scbond_it1.481
r_scbond_other1.48
r_angle_other_deg1.18
r_mcbond_it1.071
r_mcbond_other1.051
r_chiral_restr0.074
r_bond_refined_d0.009
r_bond_other_d0.001
r_gen_planes_refined0.001
r_gen_planes_other
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 Atoms5343
Nucleic Acid Atoms
Solvent Atoms151
Heterogen Atoms130

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
pointlessdata scaling
REFMACphasing