2SBA | pdb_00002sba

SOYBEAN AGGLUTININ COMPLEXED WITH 2,6-PENTASACCHARIDE

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.2		0.1 M HEPES, PH 7.2; 1 MM CACL2; 1 MM MNCL2 0.5 M NACL

Crystal Properties
Matthews coefficient	Solvent content
5.9	79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.9	α = 90
b = 144.9	β = 90
c = 109.4	γ = 120

Symmetry
Space Group	P 64 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	287	AREA DETECTOR	SIEMENS	COLLIMATOR		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

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	2.4	90	81	0.126	0.126		3.6		17287		2	18.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	2LTN	2.6	90	17012		80	0.208

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
t_dihedral_angle_d	20.37
t_it	5.66
t_angle_deg	2.217
t_nbd	0.069
t_gen_planes	0.023
t_bond_d	0.016
t_trig_c_planes	0.007
t_incorr_chiral_ct
t_pseud_angle

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1688
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms	27

Software

Software
Software Name	Purpose
X-PLOR	model building
TNT	refinement
X-GEN	data reduction
X-GEN	data scaling
X-PLOR	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.