2WYI

Structure of the Streptococcus pyogenes family GH38 alpha-mannosidase complexed with swainsonine

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		15 MG/ML 3C CLEAVED SPGH38 MIXED WITH 3% V/V GLYCEROL, 54% V/V TACSIMATE (PH 7.0) AND 2% V/V POLYETHYLENE GLYCOL 6000

Crystal Properties
Matthews coefficient	Solvent content
3.84	69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.68	α = 90
b = 178.68	β = 90
c = 198.237	γ = 90

Symmetry
Space Group	P 43 21 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 CCD		2008-11-21	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.6	50	99.8	0.05	27.7	6.8		93181		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.69	100		0.39	4.1	7

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	MAD	THROUGHOUT	PDB ENTRY 2WYH	2.6	132.45	93181	4888	99.7	0.189	0.187	0.223	RANDOM	28.09

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]
0.89			0.89		-1.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.958
r_dihedral_angle_4_deg	19.023
r_dihedral_angle_3_deg	14.68
r_dihedral_angle_1_deg	5.724
r_scangle_it	2.041
r_scbond_it	1.193
r_angle_refined_deg	1.111
r_mcangle_it	0.782
r_mcbond_it	0.396
r_chiral_restr	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14274
Nucleic Acid Atoms
Solvent Atoms	345
Heterogen Atoms	114

Software

Software
Software Name	Purpose
PHASER	model building
SCALEPACK	data scaling
SHARP	phasing
SHELX	phasing
RESOLVE	phasing
PHASER	phasing
REFMAC	refinement