2E1Z | pdb_00002e1z

Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with diadenosine tetraphosphate (Ap4A) obtained after co-crystallization with ATP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X3M	PDB entry 1X3M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1M Bis-Tris pH 6.5, 17% (w/v) polyethylene glycol monomethyl ether 5000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.483	α = 90
b = 110.483	β = 90
c = 66.607	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	IMAGE PLATE	RIGAKU		2005-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.0	SPring-8	BL26B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.98	50	99.9	0.073	24.41	13.88		32959			45.2

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)
	1.98	2.05	100		0.494	2.19	4.9	3248

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 1X3M	1.98	30	29989	1596	95.94	0.19207	0.19055	0.19	0.22092	0.22	RANDOM	25.577

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]
1.61	0.81		1.61		-2.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.497
r_dihedral_angle_4_deg	18.982
r_dihedral_angle_3_deg	13.617
r_dihedral_angle_1_deg	5.695
r_scangle_it	2.35
r_scbond_it	1.425
r_angle_refined_deg	1.177
r_mcangle_it	1.077
r_angle_other_deg	0.89
r_mcbond_it	0.639
r_symmetry_vdw_other	0.228
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.194
r_nbd_other	0.189
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.134
r_symmetry_hbond_refined	0.12
r_mcbond_other	0.1
r_nbtor_other	0.082
r_chiral_restr	0.069
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2955
Nucleic Acid Atoms
Solvent Atoms	189
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling