5DD7

Structure of thiamine-monophosphate kinase from Acinetobacter baumannii in complex with AMPPNP and thiamine-monophosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5D9U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	Microlytic MGCS G4 optimization screen: 19% PEG 3350, 200mM KNa-tartrate, 100mM HEPES/NaOH pH 7.75; AcbaC.17905.a.B1.PW37686 at 30mg/ml with 5mM MgCl2/ANP, then over night soak with in reservoir solution with 5mM MgCl2/ANP/TMP; cryo: soak solution with 20% EG; tray 264486e7, puck RUX3-7

Crystal Properties
Matthews coefficient	Solvent content
2.17	43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.96	α = 90
b = 93.29	β = 90
c = 73.48	γ = 90

Symmetry
Space Group	P 21 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	CCD	RAYONIX MX-225		2015-08-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.7	50	99.5	0.053	0.058	22.56	6.2	66411	66088		-3	18.91

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.74	99.2		0.587	0.64	3.43	6.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5d9u	1.7	39.41	1.34	66070	2015	99.5	0.1504	0.1495	0.1769	Random selection	26.7195

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
f_dihedral_angle_d	11.37
f_angle_d	0.837
f_chiral_restr	0.055
f_bond_d	0.006
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4608
Nucleic Acid Atoms
Solvent Atoms	496
Heterogen Atoms	128

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.