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Crystal structure of E. coli aspartate transcarbamoylase in the R-state complexed with CP, succinate, ATP, and Mg2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KH0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 Protein solution: 0.016 mM ATCase in 40 mM Tris pH 7.0, 20 mM CP, 20 mM succinate, 30 mM MgCl2, and 10 mM ATP
Well solution: 0.1 M Bis-Tris pH 6.5 and 20-25% PEG 300
Drops: 0.001 mL each of protein and well solution
Crystal Properties Matthews coefficient Solvent content 3.23 61.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.049 α = 90 b = 148.793 β = 90 c = 207.866 γ = 90
Symmetry Space Group P 21 21 21
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 2021-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9795 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3 103.9 99.3 0.2676 0.1213 0.966 4.2 5.8 80502 62.34
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 1.027 0.454 0.642 0.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3 103.9 1.33 80135 1992 99.27 0.2185 0.2178 0.2216 0.2488 0.2511 71.23
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.0245 f_angle_d 0.518 f_chiral_restr 0.0425 f_plane_restr 0.0037 f_bond_d 0.0017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21457 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 480
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling PHASER phasing