2Z4T | pdb_00002z4t

Crystal Structure of Vibrionaceae Photobacterium sp. JT-ISH-224 2,6-sialyltransferase in a Ternary Complex with Donor Product CMP and Accepter Substrate Lactose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EX1	PDB ENTRY 2EX1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	298	0.2M lithium sulfate, 30% PEG4000, 0.1M Tris-HCl (pH8.5), VAPOR DIFFUSION, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
4.11	70.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.292	α = 90
b = 90.292	β = 90
c = 204.33	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	CCD	RIGAKU JUPITER 210			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.000	SPring-8	BL38B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.5	50	99.8	0.082	0.082	20	5.4		34277

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59	100		0.432	0.432	3.7	5.5

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 2EX1	2.5	41.31	32443	32443	1727	99.84	0.19467	0.19217	0.19	0.24297	0.24	RANDOM	44.646

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]
-0.2	-0.1		-0.2		0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.912
r_dihedral_angle_4_deg	26.286
r_dihedral_angle_3_deg	18.12
r_dihedral_angle_1_deg	14.288
r_scangle_it	2.648
r_angle_refined_deg	1.882
r_scbond_it	1.626
r_mcangle_it	1.196
r_mcbond_it	0.657
r_nbtor_refined	0.316
r_nbd_refined	0.231
r_symmetry_vdw_refined	0.23
r_chiral_restr	0.18
r_symmetry_hbond_refined	0.159
r_xyhbond_nbd_refined	0.157
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3955
Nucleic Acid Atoms
Solvent Atoms	281
Heterogen Atoms	87

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing