9KPY | pdb_00009kpy

Structure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter spp. with the expression tag bound in the substrate binding site of a neighbouring molecule at 2.20 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
2.64	53.42

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)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.2	41.581	97.3	0.132	0.187	0.132	0.98	3.6	2.1		56390			33.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.26			0.725	1.024	0.723	0.395	1.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.2	41.581	56389	1135	96.847	0.208	0.207	0.2129	0.267	0.2691	42.442

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]
1.931		0.099	0.739		-2.666

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.652
r_dihedral_angle_3_deg	13.135
r_lrange_it	10.142
r_lrange_other	10.142
r_dihedral_angle_2_deg	9.389
r_dihedral_angle_1_deg	6.437
r_scangle_it	5.813
r_scangle_other	5.812
r_mcangle_it	4.874
r_mcangle_other	4.874
r_scbond_it	3.589
r_scbond_other	3.588
r_mcbond_it	3.061
r_mcbond_other	3.059
r_angle_refined_deg	1.368
r_angle_other_deg	0.732
r_nbd_other	0.243
r_symmetry_nbd_other	0.213
r_nbd_refined	0.209
r_symmetry_nbd_refined	0.202
r_symmetry_xyhbond_nbd_refined	0.192
r_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.175
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_other	0.083
r_chiral_restr	0.063
r_bond_refined_d	0.005
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	7704
Nucleic Acid Atoms
Solvent Atoms	561
Heterogen Atoms	86

Software

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