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Thermotoga maritima threonylcarbamoyl adenylate synthase (TsaC2) in complex with N-carboxy-L-threonine, magnesium and pyrophosphate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q9WZV6-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.4 294.15 Reservoir 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 coefficient Solvent content 3.9 68.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.039 α = 90 b = 154.039 β = 90 c = 87.241 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS EIGER X 9M 2024-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X17B1 0.920105 NSLS X17B1
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.277 34.09 99.1 0.374 0.39 0.108 0.3 7.7 12.8 54251
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) Redundancy Number Unique Reflections (All) 1 2.277 2.317 100 3.685 3.836 1.06 0.419
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2.28 34.09 51476 2724 98.97 0.18873 0.18747 0.1913 0.21246 0.1859 RANDOM 47.005
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] 0.23 0.11 0.23 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.787 r_dihedral_angle_4_deg 21.551 r_dihedral_angle_3_deg 17.684 r_dihedral_angle_1_deg 7.248 r_long_range_B_refined 4.848 r_long_range_B_other 4.848 r_scangle_other 2.405 r_mcangle_other 1.761 r_mcangle_it 1.76 r_angle_refined_deg 1.563
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.787 r_dihedral_angle_4_deg 21.551 r_dihedral_angle_3_deg 17.684 r_dihedral_angle_1_deg 7.248 r_long_range_B_refined 4.848 r_long_range_B_other 4.848 r_scangle_other 2.405 r_mcangle_other 1.761 r_mcangle_it 1.76 r_angle_refined_deg 1.563 r_scbond_it 1.481 r_scbond_other 1.48 r_angle_other_deg 1.18 r_mcbond_it 1.071 r_mcbond_other 1.051 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_bond_other_d 0.001 r_gen_planes_refined 0.001 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 Atoms Number Protein Atoms 5343 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling REFMAC phasing