5CC8 | pdb_00005cc8

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

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	native crystal: JCSG+ g10 30% PEG 2000 MME, 150mM KBr; AnphA.17905.a.B1.PW37686 at 25mg/ml, 6mM each MgCl2; cryo: 20% EG, 5mM Mg/AMPPNP; tray 263060g10, puck ute6-5; iodide crystal: JCSG+ b2: 20% PEG 3350, 200mM NaSCN; AnphA.17905.a.B1.PW37686 at 25mg/ml, 6mM each MgCl2, AMPPNP; cryo: soak in 10% and 20% of a 2.5M NaI solution in EG added to reservoir solution, 10 sec soaks each; tray 263060b2, puck hmh9-1

Crystal Properties
Matthews coefficient	Solvent content
2.14	46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.14	α = 90
b = 93.76	β = 90
c = 72.49	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	RIGAKU SATURN 944+		2015-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	1.75	50	99.8	0.051	0.052	33.71	14.23		60460		-3	17.54

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	1.75	1.8	99.9		0.577	0.617	3.87	8.29

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	iodide soak	1.75	47.905	1.99	60437	3078	99.79	0.1606	0.1589	0.16	0.1936	0.19	Random selection	24.0567

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	11.181
f_angle_d	1.016
f_chiral_restr	0.049
f_bond_d	0.006
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4424
Nucleic Acid Atoms
Solvent Atoms	551
Heterogen Atoms	74

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
ARP	model building
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.