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Crystal structure of E. coli aspartate transcarbamoylase in the R-state complexed with PALA, ATP, GTP, 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 7 295 Protein solution: 0.016 mM ATCase in 40 mM Tris pH 7.5, 15 mM MgCl2, 1 mM TCEP, 10 mM ATP, 2 mM GTP, and 2 mM N-phosphonacetyl-L-aspartate (PALA)
Well solution: Tacsimate pH 7.0 and 9-14% (w/v) PEG 3350
Seed solutions: 10- and 100-fold dilutions were made from a 0.5 mL seed stock prepared by combining two crystallization drops with well solution (21% w/v PEG 3350).
Drops: 0.001 mL well solution, 0.001 mL 10- or 100-fold diluted seed solution, 0.002 mL protein solution
Crystal Properties Matthews coefficient Solvent content 3.22 61.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.436 α = 90 b = 122.436 β = 90 c = 153.031 γ = 120
Symmetry Space Group P 3 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 295 PIXEL DECTRIS EIGER2 X 16M 2023-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE 7B2 0.9185 CHESS 7B2
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 2.19 62.05 98.9 0.086 0.041 0.994 13.9 5.2 67983 44.22
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 2.19 2.27 0.808 0.378 0.705 1.3
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 2.19 62.05 1.34 67947 1364 98.86 0.1459 0.1454 0.1474 0.1681 0.169 60.03
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 14.6698 f_angle_d 0.8066 f_chiral_restr 0.0516 f_plane_restr 0.0075 f_bond_d 0.0058
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7182 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 162
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling PHASER phasing