9EEH | pdb_00009eeh

Crystal structure of E. coli aspartate transcarbamoylase in the R-state complexed with PALA, ATP, GTP, and Mg2+

X-RAY DIFFRACTION

---

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