2E20 | pdb_00002e20

Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with diadenosine tetraphosphate (Ap4A)

X-RAY DIFFRACTION

---

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, 45% (v/v) pentaerythritol ethoxylate (15/4 EO/OH), 100mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.56	α = 90
b = 110.56	β = 90
c = 66.612	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	MAR scanner 345 mm plate	Osmic mirror	2006-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	2.4	30	99.2	0.074	22.1	31.48		18755			58.02

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)
	2.4	2.49	95.2		0.413	3.05		1775

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	2.4	30	17574	945	99.28	0.20194	0.19943	0.2	0.25193	0.25	RANDOM	38.022

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]
2.98	1.49		2.98		-4.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.522
r_dihedral_angle_4_deg	15.339
r_dihedral_angle_3_deg	14.006
r_dihedral_angle_1_deg	5.859
r_scangle_it	1.613
r_angle_refined_deg	1.145
r_scbond_it	1.07
r_angle_other_deg	0.88
r_mcangle_it	0.781
r_mcbond_it	0.705
r_symmetry_vdw_other	0.223
r_nbd_refined	0.192
r_nbd_other	0.185
r_nbtor_refined	0.167
r_symmetry_vdw_refined	0.143
r_xyhbond_nbd_refined	0.136
r_symmetry_hbond_refined	0.125
r_nbtor_other	0.084
r_mcbond_other	0.075
r_xyhbond_nbd_other	0.067
r_chiral_restr	0.063
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2938
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling