4U8E

Crystal structure of 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase from Streptococcus agalactiae

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	15% polyethylene glycol 10,000, 2% dioxane, and 0.1 M sodium citrate (pH 6.5)

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.234	α = 90
b = 87.968	β = 90
c = 90.295	γ = 90

Symmetry
Space Group	I 2 2 2

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 315		2011-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1	SPring-8	BL38B1

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	50	100	28.6	6		14717

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2PPW	2	45.15	13926	737	99.05	0.18164	0.17942	0.22491	RANDOM	27.179

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]
-0.01			-0.05		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.777
r_dihedral_angle_4_deg	26.866
r_dihedral_angle_3_deg	11.378
r_dihedral_angle_1_deg	4.484
r_long_range_B_refined	2.839
r_long_range_B_other	2.741
r_scangle_other	1.426
r_mcangle_it	1.244
r_mcangle_other	1.243
r_angle_refined_deg	0.934
r_scbond_it	0.822
r_scbond_other	0.821
r_mcbond_it	0.743
r_mcbond_other	0.742
r_angle_other_deg	0.72
r_chiral_restr	0.053
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1656
Nucleic Acid Atoms
Solvent Atoms	121
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement