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Thermotoga maritima threonylcarbamoyl adenylate synthase (TsaC2) in complex with L-threonine, magnesium and ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9D3H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.2 294.15 Reservoir solution: 80 mM sodium cacodylate, 110-160 mM calcium acetate, 14% PEG8000, 20% glycerol, final pH 6.2.
Sample: 25 mg/ml TmTsaC2, 50 mM Tris (pH 7.5), 50 mM KCl and 1 mM DTT, 10 mM L-threonine, 1 mM AMPCPP and 1 mM MgCl2.
Drop: 1.5 reservoir + 1.5 ul sample.
Crystal soaked 10 min in 40% glycerol, 14.4% PEG8000, 80 mM sodium cacodylate, 160 mM sodium acetate, 10 mM L-threonine, 10 mM ATP, 10 mM MgCl2, 10 mM NaHCO3, pH 6.2
Crystal Properties Matthews coefficient Solvent content 3.89 68.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.764 α = 90 b = 153.764 β = 90 c = 87.207 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 PILATUS 6M 2024-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.19499 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.25 44.43 99.9 0.556 0.124 0.953 6.61 19.6 56743
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.29 1.806 0.446 0.884
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 2.25 44.43 45571 2356 84.44 0.18493 0.18316 0.193 0.21894 0.2224 RANDOM 47.368
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] -0.03 -0.01 -0.03 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.693 r_dihedral_angle_4_deg 19.716 r_dihedral_angle_3_deg 18.167 r_long_range_B_refined 9.976 r_long_range_B_other 9.976 r_scangle_other 8.407 r_dihedral_angle_1_deg 7.669 r_scbond_it 6.326 r_scbond_other 6.326 r_mcangle_it 5.693
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.693 r_dihedral_angle_4_deg 19.716 r_dihedral_angle_3_deg 18.167 r_long_range_B_refined 9.976 r_long_range_B_other 9.976 r_scangle_other 8.407 r_dihedral_angle_1_deg 7.669 r_scbond_it 6.326 r_scbond_other 6.326 r_mcangle_it 5.693 r_mcangle_other 5.692 r_mcbond_it 4.24 r_mcbond_other 4.156 r_angle_refined_deg 1.586 r_angle_other_deg 1.194 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 5132 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling REFMAC phasing