9GGJ | pdb_00009ggj

Crystal structure of argininosuccinate lyase from Arabidopsis thaliana (AtASL) in complex with biological substrate and products - argininosuccinate, argnine and fumarate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9GGI	Earlier solved unliganded structure of AtASL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	294	2.0M Ammonium sulfate, pH 5.5 0.1 M Bis-TRIS, crystal soaked for 20 minutes in 20mM solution of argininosuccinate in mother liquor and 25% (v/v) glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.33	63.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.588	α = 90
b = 230.848	β = 89.48
c = 112.534	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER X 16M		2023-08-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.976	PETRA III, EMBL c/o DESY	P13 (MX1)

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	49.573	90.38	0.206	0.116	0.9859	4.25	4.25		260782

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	2.114	70.11		0.832	0.459	0.54	1.8

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	MOLECULAR REPLACEMENT	THROUGHOUT	2	49.57	258807	1974	71.6	0.17583	0.17544	0.1861	0.22689	0.232	RANDOM	25.534

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]
-0.96		-0.02	-0.06		1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.763
r_dihedral_angle_2_deg	8.46
r_long_range_B_refined	6.725
r_long_range_B_other	6.614
r_dihedral_angle_1_deg	6.102
r_scangle_other	4.295
r_scbond_it	2.761
r_scbond_other	2.65
r_mcangle_it	2.627
r_mcangle_other	2.627
r_angle_refined_deg	1.751
r_mcbond_it	1.654
r_mcbond_other	1.654
r_angle_other_deg	0.581
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
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	28384
Nucleic Acid Atoms
Solvent Atoms	2957
Heterogen Atoms	142

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
STARANISO	data scaling
PHASER	phasing