8I8J

Crystal structure of the ternary complex of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter sp. with Coenzyme-A and Phosphonoacetic acid at 2.07 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	54.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.966	α = 90
b = 78.659	β = 93.121
c = 107.027	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	2.07	41.55	96.8	0.989	3.1	2.1		68615			44.9

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	2.07	2.13			0.182

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	2.07	41.546	67601	1014	96.837	0.226	0.2254	0.2766	51.94

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]
0.003		-0.001	-0.002		-0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.744
r_dihedral_angle_6_deg	14.408
r_lrange_it	9.696
r_lrange_other	9.692
r_dihedral_angle_2_deg	9.2
r_dihedral_angle_1_deg	6.838
r_scangle_it	6.777
r_scangle_other	6.776
r_mcangle_it	5.648
r_mcangle_other	5.647
r_scbond_it	4.278
r_scbond_other	4.277
r_mcbond_it	3.632
r_mcbond_other	3.632
r_angle_refined_deg	1.253
r_angle_other_deg	0.689
r_dihedral_angle_other_2_deg	0.545
r_nbd_other	0.237
r_nbd_refined	0.219
r_symmetry_nbd_other	0.219
r_symmetry_nbd_refined	0.214
r_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.179
r_symmetry_xyhbond_nbd_refined	0.177
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.056
r_symmetry_xyhbond_nbd_other	0.051
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_gen_planes_other	0.005
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