23FH | pdb_000023fh

Crystal structure of short-form adenosine triphosphate phosphoribosyltransferase from Acinetobacter baumannii at 2.18 angstrom 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 formate

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.75

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)	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	2.18	97.78	99.6	0.062	0.073	0.038	0.999	13.1	6.7		29519			54.9

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	2.18	2.25			1.497	1.763	0.924	0.744	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	29464	739	99.561	0.18	0.1791	0.1906	0.2116	0.2183	65.915

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]
1.58			3.2		-4.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.63
r_dihedral_angle_6_deg	14.098
r_dihedral_angle_2_deg	13.035
r_lrange_it	13.004
r_lrange_other	12.983
r_scangle_it	9.826
r_scangle_other	9.824
r_mcangle_it	7.496
r_mcangle_other	7.495
r_dihedral_angle_1_deg	7.394
r_scbond_it	6.491
r_scbond_other	6.491
r_mcbond_it	5.227
r_mcbond_other	5.226
r_angle_refined_deg	1.551
r_angle_other_deg	0.498
r_nbd_other	0.234
r_nbd_refined	0.222
r_xyhbond_nbd_refined	0.209
r_symmetry_nbd_other	0.207
r_nbtor_refined	0.172
r_symmetry_xyhbond_nbd_other	0.164
r_symmetry_nbd_refined	0.143
r_symmetry_xyhbond_nbd_refined	0.115
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.068
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3502
Nucleic Acid Atoms
Solvent Atoms	244
Heterogen Atoms	22

Software

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