8ZN3

Structure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter sp. with the expression tag bound in the substrate binding site of a neighbouring molecule at 2.41 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
2.71	54.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.692	α = 90
b = 78.682	β = 93.077
c = 106.902	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)	R Merge I (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	2.41	106.75	94.4	0.194	0.975	4.8	2.2		41591			36

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.41	2.5	87.4		1.019	0.391	1.1	2.2

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	2.41	106.748	41591	2078	93.804	0.211	0.2086	0.2627	46.791

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]
1.303		0.11	1.58		-2.879

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.405
r_dihedral_angle_3_deg	13.347
r_lrange_other	10.297
r_lrange_it	10.295
r_dihedral_angle_2_deg	9.371
r_dihedral_angle_1_deg	6.701
r_scangle_it	6.316
r_scangle_other	6.315
r_mcangle_it	5.857
r_mcangle_other	5.857
r_scbond_it	3.722
r_scbond_other	3.722
r_mcbond_it	3.528
r_mcbond_other	3.528
r_angle_refined_deg	1.375
r_angle_other_deg	0.739
r_nbd_other	0.241
r_symmetry_nbd_other	0.212
r_nbd_refined	0.208
r_symmetry_nbd_refined	0.202
r_symmetry_xyhbond_nbd_refined	0.195
r_xyhbond_nbd_refined	0.192
r_nbtor_refined	0.174
r_symmetry_xyhbond_nbd_other	0.086
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.061
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7662
Nucleic Acid Atoms
Solvent Atoms	519
Heterogen Atoms	68

Software

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