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Thermotoga maritima threonylcarbamoyl adenylate synthase (TsaC2) in complex with N-carboxy-L-threonine, magnesium and ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9DG5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 13.5% PEG8000, 20% glycerol, 230 mM sodium acetate, 80 mM sodium cacodylate, pH 7.4, 25 mg/ml TmTsaC2, 10 mM threonine, 30 mM NaHCO3.
Crystal Properties Matthews coefficient Solvent content 3.87 68.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.596 α = 90 b = 153.596 β = 90 c = 86.553 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 100 PIXEL DECTRIS PILATUS 6M 2024-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.97741 ALS 5.0.2
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 2.01 44.38 100 0.244 0.252 0.063 0.998 10.7 15.9 78278
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 2.01 2.05 100 4.044 4.175 1.032 0.308 0.8 16.1
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 2.01 44.38 74298 3941 99.97 0.19446 0.19331 0.2021 0.21647 0.2233 RANDOM 45.031
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] 0.73 0.36 0.73 -2.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.462 r_long_range_B_refined 13.415 r_long_range_B_other 13.415 r_scangle_other 11.941 r_scbond_it 9.304 r_scbond_other 9.303 r_mcangle_it 8.542 r_mcangle_other 8.542 r_mcbond_it 6.825 r_mcbond_other 6.795
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.462 r_long_range_B_refined 13.415 r_long_range_B_other 13.415 r_scangle_other 11.941 r_scbond_it 9.304 r_scbond_other 9.303 r_mcangle_it 8.542 r_mcangle_other 8.542 r_mcbond_it 6.825 r_mcbond_other 6.795 r_dihedral_angle_1_deg 6.783 r_dihedral_angle_2_deg 6.449 r_angle_refined_deg 1.27 r_angle_other_deg 0.436 r_chiral_restr 0.061 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 5142 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing