4XH1

Crystal structure of Salmonella typhimurium propionate kinase in complex with AMPPNP and propionate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2E1Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293.15	0.1 M Bis-Tris pH 6.5, polyethylene glycol 2000

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.61	α = 90
b = 111.61	β = 90
c = 66.65	γ = 120

Symmetry
Space Group	P 31 2 1

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	MARMOSAIC 225 mm CCD		2014-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.976	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	32.22	99	0.071	17	7.4		32233			31.469

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.11	98.5		0.507	4	7.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	THROUGHOUT	2E1Y	2	32.22	30589	1634	98.77	0.18227	0.17995	0.22615	RANDOM	34.912

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_2_deg	35.667
r_dihedral_angle_4_deg	22.41
r_dihedral_angle_3_deg	14.613
r_long_range_B_refined	7.424
r_long_range_B_other	7.423
r_dihedral_angle_1_deg	6.677
r_scangle_other	6.006
r_mcangle_it	4.533
r_mcangle_other	4.533
r_scbond_it	4.129
r_scbond_other	4.128
r_mcbond_it	3.375
r_mcbond_other	3.368
r_angle_refined_deg	1.953
r_angle_other_deg	0.909
r_chiral_restr	0.116
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2923
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PHASER	phasing
Coot	model building
iMOSFLM	data reduction