2WMK

Crystal structure of the catalytic module of a family 98 glycoside hydrolase from Streptococcus pneumoniae SP3-BS71 (Sp3GH98) in complex with the A-LewisY pentasaccharide blood group antigen.

X-RAY DIFFRACTION

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Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.34	46.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.9	α = 90
b = 153.7	β = 90
c = 90.88	γ = 90

Symmetry
Space Group	P 21 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	292	CCD	ADSC QUANTUM 315r			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1		SSRL	BL7-1

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	1.9	40	99.1	0.11	14.5	6.7		102091		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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	OTHER	THROUGHOUT	NONE	1.9	29.12	102091	5371	99.03	0.16481	0.16248	0.16	0.2096	0.21	RANDOM	12.809

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	36.859
r_dihedral_angle_4_deg	21.562
r_dihedral_angle_3_deg	14.199
r_dihedral_angle_1_deg	6.934
r_scangle_it	4.01
r_scbond_it	2.694
r_angle_refined_deg	1.666
r_mcangle_it	1.645
r_mcbond_it	1.117
r_nbtor_refined	0.313
r_nbd_refined	0.212
r_symmetry_hbond_refined	0.196
r_xyhbond_nbd_refined	0.164
r_symmetry_vdw_refined	0.159
r_chiral_restr	0.132
r_bond_refined_d	0.019
r_gen_planes_refined	0.008
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_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	9359
Nucleic Acid Atoms
Solvent Atoms	974
Heterogen Atoms	120

Software

Software
Software Name	Purpose
REFMAC	refinement