2IIQ

Crystal structure of Pasteurella multocida sialyltransferase in an open conformation with CMP bound

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EX0	PDB ENTRY 2EX0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	25%, PEG 3350, 0.1 M NaCl, 0.1 M HEPES, 0.4% Triton X-100 streak seeded by apo crystals, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.528	α = 90
b = 61.572	β = 94.77
c = 119.547	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	BRUKER SMART 6000		2006-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	59.55	99.76	0.1001	5.35	6.16	39043	38951			20.54

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.3	100		0.2421	1.78		4884

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	PDB ENTRY 2EX0	2.3	59.55	32366	1705	99.95	0.21006	0.20766	0.25554	RANDOM	5.84

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]
-0.67		-0.23	0.39		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.37
r_dihedral_angle_4_deg	17.027
r_dihedral_angle_3_deg	16.779
r_dihedral_angle_1_deg	6.612
r_scangle_it	1.982
r_angle_refined_deg	1.348
r_scbond_it	1.24
r_mcangle_it	0.814
r_mcbond_it	0.506
r_nbtor_refined	0.304
r_symmetry_hbond_refined	0.249
r_nbd_refined	0.216
r_symmetry_vdw_refined	0.215
r_xyhbond_nbd_refined	0.184
r_chiral_restr	0.094
r_bond_refined_d	0.012
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	6331
Nucleic Acid Atoms
Solvent Atoms	569
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data collection
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
AMoRE	phasing