3JUL | pdb_00003jul

Crystal structure of Listeria innocua D-Tagatose-6-Phosphate Kinase bound with substrate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HIC	PDB ENTRY 3HIC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5	298	25% PEG 3350, 0.2M MgCl2, 0.1M Tris pH 8.5, 8mM Fructose-6-Phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.307	α = 90
b = 44.24	β = 104.65
c = 79.116	γ = 90

Symmetry
Space Group	C 1 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	ADSC QUANTUM 210	MIRRORS	2009-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C		NSLS	X12C

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	2.2	50	99.1	0.097	7.9	6.4		14658			21.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.2	2.28	94.3		0.591	5.3	5.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3HIC	2.4	40.78	10640	10640	439	94.5	0.226	0.226	0.21	0.267	0.26	RANDOM	35.2

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]
-6.177		11.758	5.576		0.601

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	3.242
c_mcangle_it	2.325
c_scbond_it	2.324
c_mcbond_it	1.377
c_angle_deg	1.3
c_bond_d	0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2265
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms	17

Software

Software
Software Name	Purpose
CBASS	data collection
MOLREP	phasing
CNS	refinement
DENZO	data reduction
HKL-2000	data scaling