8JUK | pdb_00008juk

Crystal structure of Adenosine triphosphate phosphoribosyltransferase from Acinetobacter baumannii at 2.18 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7WGM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	Sodium acetate trihydrate; Sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.476	α = 90
b = 79.203	β = 90
c = 97.777	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER2 X 9M		2023-03-01	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	2.18	97.78	99.6	0.999	14	6.7		29519

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	2.18	2.25	98.8		0.74	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	2.181	57.769	29465	1499	99.564	0.188	0.1845	0.2	0.2466	0.26	66.607

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]
1.529			3.233		-4.761

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.204
r_dihedral_angle_2_deg	14.979
r_dihedral_angle_6_deg	13.383
r_lrange_other	13.067
r_lrange_it	13.048
r_scangle_it	9.454
r_scangle_other	9.452
r_mcangle_it	7.42
r_mcangle_other	7.419
r_dihedral_angle_1_deg	7.3
r_scbond_it	6.279
r_scbond_other	6.278
r_mcbond_it	5.161
r_mcbond_other	5.157
r_angle_refined_deg	1.251
r_angle_other_deg	0.4
r_xyhbond_nbd_refined	0.239
r_nbd_other	0.236
r_nbd_refined	0.219
r_symmetry_xyhbond_nbd_other	0.218
r_symmetry_xyhbond_nbd_refined	0.217
r_symmetry_nbd_other	0.208
r_nbtor_refined	0.169
r_symmetry_nbd_refined	0.129
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.055
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3518
Nucleic Acid Atoms
Solvent Atoms	248
Heterogen Atoms	10

Software

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