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Thermotoga maritima threonylcarbamoyl adenylate synthase (TsaC2) in complex with L-threonine
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 14% PEG8000, 20% glycerol, 150 mM calcium acetate, 80 mM sodium cacodylate, pH 6.5, 25 mg/mL TmTsaC2, 50 mM Tris, pH 7.5, 50 mM KCl, 1 mM DTT, 10 mM L-threonine, 1 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 3.86 68.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.672 α = 90 b = 153.672 β = 90 c = 86.733 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 PILATUS3 2M 2023-08-16 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) 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 2.05 44.5 99.9 0.244 0.247 0.04 0.999 16 35.3 73986
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 2.05 2.09 0.87 0.247 0.04 0.366
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 2.05 44.4 64297 3283 91.17 0.18993 0.18932 0.1982 0.20183 0.2039 RANDOM 31.737
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] 0.18 0.09 0.18 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.893 r_dihedral_angle_2_deg 9.391 r_long_range_B_refined 7.606 r_long_range_B_other 7.605 r_dihedral_angle_1_deg 6.776 r_scangle_other 5.547 r_mcangle_it 3.998 r_mcangle_other 3.997 r_scbond_it 3.357 r_scbond_other 3.356
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.893 r_dihedral_angle_2_deg 9.391 r_long_range_B_refined 7.606 r_long_range_B_other 7.605 r_dihedral_angle_1_deg 6.776 r_scangle_other 5.547 r_mcangle_it 3.998 r_mcangle_other 3.997 r_scbond_it 3.357 r_scbond_other 3.356 r_mcbond_it 2.486 r_mcbond_other 2.481 r_angle_refined_deg 1.389 r_angle_other_deg 0.464 r_chiral_restr 0.067 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_dihedral_angle_4_deg r_gen_planes_refined 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 5144 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling REFMAC phasing