6WYX

Crystal structure of Pseudomonas 7A Glutaminase-Asparaginase in complex with L-Asp at pH 5.0

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4PGA	PDB entry 4PGA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	8% w/v Tacsimate, pH 5.0, 20% w/v PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.958	α = 90
b = 80.958	β = 90
c = 176.819	γ = 120

Symmetry
Space Group	P 31

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		2019-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

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	1.48	35.1	99.8	0.076	0.027	0.996	27.4	8.3		216530

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	1.48	1.52	98.3		0.737	0.349	0.732	2.2	4.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 4PGA	1.48	35.06	204714	3013	96.08	0.0881	0.0876	0.1199	RANDOM	16.109

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]
-1.39			-1.39		2.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.586
r_sphericity_free	27.926
r_dihedral_angle_4_deg	15.016
r_dihedral_angle_3_deg	12.881
r_sphericity_bonded	12.245
r_dihedral_angle_1_deg	6.187
r_rigid_bond_restr	3.013
r_angle_refined_deg	1.89
r_angle_other_deg	1.072
r_chiral_restr	0.122

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.586
r_sphericity_free	27.926
r_dihedral_angle_4_deg	15.016
r_dihedral_angle_3_deg	12.881
r_sphericity_bonded	12.245
r_dihedral_angle_1_deg	6.187
r_rigid_bond_restr	3.013
r_angle_refined_deg	1.89
r_angle_other_deg	1.072
r_chiral_restr	0.122
r_bond_refined_d	0.018
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9620
Nucleic Acid Atoms
Solvent Atoms	1244
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.