2ZWI | pdb_00002zwi

Crystal structure of alpha/beta-Galactoside alpha-2,3-Sialyltransferase from a Luminous Marine Bacterium, <I>Photobacterium phosphoreum</I>

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z4T	PDB ENTRY 2Z4T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	22% PEG3350, 0.2M KCl, 2mM ZnSO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.429	α = 90.06
b = 57.827	β = 106.76
c = 59.246	γ = 103.2

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	RIGAKU JUPITER 210			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	97.8	13.804	2	43495	43495			17.685

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 2Z4T	2.01	20.69	41296	41296	2192	97.46	0.17574	0.17296	0.17	0.22834	0.23	RANDOM	17.685

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.804
r_dihedral_angle_4_deg	16.321
r_dihedral_angle_3_deg	14.437
r_dihedral_angle_1_deg	5.227
r_scangle_it	2.507
r_scbond_it	1.589
r_angle_refined_deg	1.204
r_mcangle_it	1.05
r_mcbond_it	0.613
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.222
r_nbd_refined	0.2
r_symmetry_hbond_refined	0.195
r_xyhbond_nbd_refined	0.136
r_symmetry_metal_ion_refined	0.123
r_metal_ion_refined	0.102
r_chiral_restr	0.088
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
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	6003
Nucleic Acid Atoms
Solvent Atoms	366
Heterogen Atoms	102

Software

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