2E1Y | pdb_00002e1y

Crystal structure of propionate kinase (TdcD) from Salmonella typhimurium

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	Microbatch method	6.5	293	0.1 Bis-Tris pH 6.5, 30% (v/v) pentaerythritol ethoxylate (15/4 EO/OH), Microbatch method, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.811	α = 90
b = 110.811	β = 90
c = 66.533	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	2005-11-29	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	2.6	30	98.3	0.101	9.7	33.56		14818			57.3

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)
	2.6	2.69	84.3		0.45	2.2		1235

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	2.6	30	13415	706	95.52	0.2022	0.19966	0.2	0.25311	0.25	RANDOM	34.052

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]
2.1	1.05		2.1		-3.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.526
r_dihedral_angle_4_deg	19.877
r_dihedral_angle_3_deg	13.691
r_dihedral_angle_1_deg	5.554
r_scangle_it	1.199
r_angle_refined_deg	0.932
r_angle_other_deg	0.809
r_mcangle_it	0.697
r_scbond_it	0.685
r_mcbond_it	0.387
r_nbd_refined	0.198
r_symmetry_vdw_other	0.19
r_nbd_other	0.178
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.142
r_symmetry_hbond_refined	0.116
r_symmetry_vdw_refined	0.111
r_nbtor_other	0.081
r_chiral_restr	0.054
r_mcbond_other	0.041
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2944
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms

Software

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