2QF8

Crystal structure of the complex of Buffalo Secretory Glycoprotein with tetrasaccharide at 2.8A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2O9O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	298	TRIS-HCL, NACL, 19% ETHANOL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.73	55.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.87	α = 90
b = 66.499	β = 90
c = 107.126	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	IMAGE PLATE	MARRESEARCH	Mirror	2007-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.54

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	2.8	56.8	5	0.143	4.97	4.65	11568	10690			50.1

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	2.8	2.9			0.143	4.97	4.65

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2O9O	2.8	56.8	10179	508	92.41	0.18885	0.18885	0.18693	0.22697	RANDOM	30.902

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]
-0.87			-0.3		1.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	22.635
r_scangle_it	5.747
r_dihedral_angle_1_deg	3.656
r_scbond_it	3.497
r_angle_refined_deg	2.563
r_mcangle_it	2.399
r_mcbond_it	1.277
r_nbd_refined	0.281
r_symmetry_vdw_refined	0.277
r_xyhbond_nbd_refined	0.262

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	22.635
r_scangle_it	5.747
r_dihedral_angle_1_deg	3.656
r_scbond_it	3.497
r_angle_refined_deg	2.563
r_mcangle_it	2.399
r_mcbond_it	1.277
r_nbd_refined	0.281
r_symmetry_vdw_refined	0.277
r_xyhbond_nbd_refined	0.262
r_symmetry_hbond_refined	0.225
r_chiral_restr	0.194
r_bond_refined_d	0.025
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2894
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	71

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.