8Y1J

Structure of the pyridoxal 5'-phosphate-dependent (PLP) threonine deaminase ilvA1 from Pseudomonas aeruginosa PAO1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TDJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.6	293	15% (w/v) PEG-6000, 0.1 M Bicine/sodium hydroxide

Crystal Properties
Matthews coefficient	Solvent content
3.27	62.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.062	α = 90
b = 114.062	β = 90
c = 191.45	γ = 120

Symmetry
Space Group	P 31 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	100	PIXEL	DECTRIS PILATUS 6M		2019-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97853	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	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	2.3	50	100	0.031	25.2	10		64851

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.34			0.287

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.3	35.73	62420	1992	99.34	0.1735	0.17261	0.20174	RANDOM	48.36

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]
0.09	0.05		0.09		-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.783
r_dihedral_angle_2_deg	10.835
r_dihedral_angle_1_deg	6.754
r_long_range_B_refined	5.068
r_long_range_B_other	5.042
r_scangle_other	2.92
r_mcangle_it	2.37
r_mcangle_other	2.37
r_scbond_it	1.712
r_scbond_other	1.712
r_mcbond_it	1.412
r_mcbond_other	1.412
r_angle_refined_deg	1.261
r_angle_other_deg	0.455
r_chiral_restr	0.059
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7754
Nucleic Acid Atoms
Solvent Atoms	370
Heterogen Atoms	21

Software

Software
Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement