2ITM | pdb_00002itm

Crystal structure of the E. coli xylulose kinase complexed with xylulose

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6	298	Drops containing equal volume of 26 mg/ml protein solution and precipitant solution comprising of 1.5 M ammonium sulfate, 50 mM sodium citrate, 1% w/v t-butanol, suspended over a 1 ml reservoir containing the precipitant solution, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.00

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.883	α = 90
b = 112.605	β = 90
c = 143.073	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC QUANTUM 315		2004-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2		SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.1	29.85	96.4				58656		1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	30	89.88

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MIR	THROUGHOUT	2.1	29.85	56530	2278	96.4	0.204	0.201	0.21	0.263	0.27	RANDOM	31.4

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]
1.22			-2.27		1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.141
r_dihedral_angle_4_deg	22.7
r_dihedral_angle_3_deg	21.822
r_scangle_it	15.279
r_scbond_it	13.8
r_dihedral_angle_1_deg	10.056
r_mcangle_it	9.35
r_mcbond_it	8.482
r_angle_other_deg	4.313
r_mcbond_other	4.074
r_angle_refined_deg	1.332
r_chiral_restr	0.34
r_symmetry_vdw_other	0.337
r_nbd_other	0.313
r_symmetry_vdw_refined	0.302
r_nbd_refined	0.286
r_xyhbond_nbd_refined	0.268
r_xyhbond_nbd_other	0.256
r_symmetry_hbond_refined	0.211
r_nbtor_refined	0.201
r_nbtor_other	0.119
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d
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	7257
Nucleic Acid Atoms
Solvent Atoms	431
Heterogen Atoms	42

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
CNS	phasing