8I8I

Crystal structure of Phosphopantetheine adenylyltransferase from Klebsiella pneumoniae at 2.59 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B6T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	0.1M HEPES pH 7.5, 20% PEG 10000

Crystal Properties
Matthews coefficient	Solvent content
2.5	51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.819	α = 90
b = 72.819	β = 90
c = 200.365	γ = 90

Symmetry
Space Group	P 41 21 2

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 PILATUS 6M		2021-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87	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	2.59	41.27	99.7	0.998	3.21	4		17572			48.8

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	2.59	2.67			0.88

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	2.59	41.27	17572	632	99.949	0.21	0.2079	0.2549	55.056

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]
					-0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.267
r_dihedral_angle_3_deg	15.562
r_lrange_other	11.15
r_lrange_it	11.133
r_scangle_it	7.42
r_scangle_other	7.419
r_mcangle_it	6.965
r_mcangle_other	6.964
r_dihedral_angle_1_deg	5.82
r_scbond_it	4.552
r_scbond_other	4.551
r_mcbond_it	4.311
r_mcbond_other	4.309
r_dihedral_angle_2_deg	3.472
r_angle_refined_deg	1.179
r_angle_other_deg	0.395
r_nbd_other	0.29
r_symmetry_nbd_refined	0.237
r_symmetry_nbd_other	0.218
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.198
r_symmetry_xyhbond_nbd_refined	0.175
r_nbtor_refined	0.171
r_symmetry_nbtor_other	0.077
r_symmetry_xyhbond_nbd_other	0.056
r_chiral_restr	0.052
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3720
Nucleic Acid Atoms
Solvent Atoms	145
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing