2IHK

crystal structure of multifunctional sialyltransferase from pasteurella multocida with CMP-3F(equatorial)-Neu5Ac bound

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	25% PEG MME 2000 0.2 M NaBr 0.4% Triton X-100, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.89	α = 90
b = 65.022	β = 98.56
c = 64.795	γ = 90

Symmetry
Space Group	P 1 21 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 315		2006-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97947	SSRL	BL11-1

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	1.9	64.96	91	0.053	0.048	13.5	2	35617	33809

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	1.9	1.95	88.9		0.177	0.204	3.8	2

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	MOLECULAR REPLACEMENT	THROUGHOUT	2EX1	1.9	32.51	33809	1792	90.02	0.17852	0.17714	0.20481	RANDOM	28.656

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]
0.06		0.09	-0.07		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.13
r_dihedral_angle_3_deg	14.224
r_dihedral_angle_4_deg	12.068
r_dihedral_angle_1_deg	5.571
r_scangle_it	2.878
r_scbond_it	1.864
r_angle_refined_deg	1.302
r_mcangle_it	1.1
r_mcbond_it	0.75
r_nbtor_refined	0.305
r_symmetry_hbond_refined	0.219
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.168
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.089
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
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	3095
Nucleic Acid Atoms
Solvent Atoms	317
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing