8I8K

Crystal structure of the ternary complex of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter sp. with Coenzyme-A and Phosphonoacetic acid at 2.13 A resolution.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8I8I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	BIS-TRIS propane pH 7.0, Sodium citrate tribasic dihydrate

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.919	α = 90
b = 78.618	β = 93.118
c = 106.981	γ = 90

Symmetry
Space Group	C 1 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 PILATUS3 2M		2022-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8731	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.127	85.31	96.3	0.982	4.7	2.1		61572			35.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.13	2.18			0.248

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.127	58.246	61571	3141	95.804	0.232	0.2306	0.2545	45.424

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]
0.016		-0.002	0.004		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.471
r_dihedral_angle_3_deg	14.382
r_lrange_it	9.852
r_lrange_other	9.85
r_dihedral_angle_2_deg	9.268
r_scangle_it	6.723
r_scangle_other	6.722
r_dihedral_angle_1_deg	6.566
r_mcangle_it	5.684
r_mcangle_other	5.684
r_scbond_it	4.191
r_scbond_other	4.191
r_mcbond_it	3.609
r_mcbond_other	3.608
r_angle_refined_deg	1.247
r_angle_other_deg	0.681
r_nbd_other	0.246
r_symmetry_nbd_other	0.216
r_nbd_refined	0.211
r_symmetry_nbd_refined	0.203
r_xyhbond_nbd_refined	0.187
r_nbtor_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.145
r_dihedral_angle_other_2_deg	0.125
r_symmetry_nbtor_other	0.082
r_symmetry_xyhbond_nbd_other	0.073
r_chiral_restr	0.062
r_gen_planes_other	0.009
r_gen_planes_refined	0.008
r_bond_refined_d	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7547
Nucleic Acid Atoms
Solvent Atoms	437
Heterogen Atoms	160

Software

Software
Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
Coot	model building