8I8M

Crystal structure of the ternary complex of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter sp. with Coenzyme-A and Phosphonoacetic acid at 2.65 A resolution.

X-RAY DIFFRACTION

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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 = 137.929	α = 90
b = 78.643	β = 93.117
c = 107.005	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	2.65	42.68	94.4	0.984	5	2.1		31523			38.3

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	2.65	2.72			0.842

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	2.651	42.64	31523	1535	94.42	0.176	0.174	0.2243	44.413

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]
0.02		0.004	0.01		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.705
r_dihedral_angle_3_deg	14.673
r_lrange_it	11.423
r_lrange_other	11.418
r_dihedral_angle_2_deg	9.564
r_scangle_it	8.046
r_scangle_other	8.046
r_mcangle_it	6.923
r_mcangle_other	6.922
r_dihedral_angle_1_deg	6.837
r_scbond_it	5.12
r_scbond_other	5.12
r_mcbond_it	4.383
r_mcbond_other	4.382
r_angle_refined_deg	1.405
r_dihedral_angle_other_2_deg	0.925
r_angle_other_deg	0.74
r_nbd_other	0.254
r_symmetry_nbd_refined	0.229
r_symmetry_nbd_other	0.219
r_nbd_refined	0.216
r_xyhbond_nbd_refined	0.198
r_nbtor_refined	0.179
r_symmetry_xyhbond_nbd_refined	0.165
r_symmetry_nbtor_other	0.082
r_symmetry_xyhbond_nbd_other	0.063
r_chiral_restr	0.059
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	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	438
Heterogen Atoms	160

Software

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