8I8L

Crystal structure of the ternary complex of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter sp. with Coenzyme-A and Phosphonoacetic acid at 2.23 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 = 137.925	α = 90
b = 78.622	β = 93.118
c = 106.985	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	2.23	42.67	96.4	0.982	5.2	2.1		53574			37.6

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	2.23	2.29			0.439

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	2.23	42.632	53561	2677	95.865	0.219	0.217	0.2614	45.892

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]
0.025		0.012	0.015		-0.041

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.867
r_dihedral_angle_6_deg	14.313
r_lrange_it	10.789
r_lrange_other	10.788
r_dihedral_angle_2_deg	9.345
r_scangle_it	7.364
r_scangle_other	7.364
r_dihedral_angle_1_deg	6.958
r_mcangle_it	6.306
r_mcangle_other	6.306
r_scbond_it	4.577
r_scbond_other	4.577
r_mcbond_it	3.972
r_mcbond_other	3.971
r_angle_refined_deg	1.391
r_angle_other_deg	0.744
r_dihedral_angle_other_2_deg	0.271
r_nbd_other	0.239
r_symmetry_nbd_other	0.219
r_nbd_refined	0.218
r_symmetry_nbd_refined	0.205
r_xyhbond_nbd_refined	0.199
r_nbtor_refined	0.179
r_symmetry_xyhbond_nbd_refined	0.147
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.06
r_symmetry_xyhbond_nbd_other	0.057
r_bond_refined_d	0.006
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	435
Heterogen Atoms	160

Software

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