8I8P | pdb_00008i8p

Crystal structure of the complex of phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Dephosphocoenzyme-A at 2.19 A resolution.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5ZZC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	1M LITHIUM SULPHATE, 2M AMMONIUM SULPHATE, 0.1M SODIUM CITRATE, PH 5.6

Crystal Properties
Matthews coefficient	Solvent content
5.76	78.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 217.038	α = 90
b = 217.038	β = 90
c = 217.038	γ = 90

Symmetry
Space Group	F 41 3 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	PSI PILATUS 6M		2018-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97199	ESRF	ID23-1

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	2.19	125.307	95.48	0.99	16.2	20		22090

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	2.19	2.25			0.631

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	2.19	125.307	22090	1044	95.582	0.203	0.2011	0.21	0.2367	0.24	63.419

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	18.635
r_dihedral_angle_3_deg	17.17
r_lrange_it	15.806
r_lrange_other	15.652
r_scangle_it	13.612
r_scangle_other	13.611
r_dihedral_angle_2_deg	13.226
r_scbond_it	9.399
r_scbond_other	9.337
r_mcangle_other	8.802
r_mcangle_it	8.764
r_dihedral_angle_1_deg	7.381
r_mcbond_it	6.455
r_mcbond_other	6.449
r_angle_refined_deg	2.068
r_dihedral_angle_other_2_deg	1.34
r_angle_other_deg	1.105
r_nbd_other	0.296
r_symmetry_nbd_refined	0.295
r_xyhbond_nbd_refined	0.292
r_symmetry_nbd_other	0.224
r_nbd_refined	0.222
r_symmetry_xyhbond_nbd_refined	0.198
r_metal_ion_refined	0.196
r_nbtor_refined	0.195
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.092
r_symmetry_xyhbond_nbd_other	0.077
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_gen_planes_other	0.008
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1305
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms	56

Software

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