8I8N

Crystal structure of the ternary complex of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter sp. with Dephosphocoenzyme-A and Phosphonoacetic acid at 2.22 A resolution.

X-RAY DIFFRACTION

---

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	54.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.268	α = 90
b = 78.418	β = 93.1
c = 106.465	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	2.22	43.18	95.2	0.966	4.3	2.2		53025			33.7

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	2.22	2.28			0.239

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	2.22	43.147	52373	2635	93.617	0.239	0.2381	0.261	47.691

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]
0.005		-0.008	-0.01		0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.339
r_dihedral_angle_3_deg	14.221
r_lrange_other	11.631
r_lrange_it	11.63
r_dihedral_angle_2_deg	11.612
r_scangle_it	7.447
r_scangle_other	7.446
r_dihedral_angle_1_deg	6.73
r_mcangle_it	6.559
r_mcangle_other	6.558
r_scbond_it	4.484
r_scbond_other	4.484
r_mcbond_it	3.991
r_mcbond_other	3.991
r_angle_refined_deg	1.26
r_angle_other_deg	0.696
r_nbd_other	0.255
r_symmetry_nbd_other	0.219
r_nbd_refined	0.211
r_symmetry_nbd_refined	0.202
r_xyhbond_nbd_refined	0.197
r_nbtor_refined	0.183
r_dihedral_angle_other_2_deg	0.157
r_symmetry_xyhbond_nbd_refined	0.136
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.067
r_symmetry_xyhbond_nbd_other	0.042
r_bond_refined_d	0.007
r_gen_planes_refined	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	484
Heterogen Atoms	146

Software

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