4MNP | pdb_00004mnp

Structure of the Sialic Acid Binding Protein from Fusobacterium Nucleatum subsp. nucleatum ATCC 25586

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3B50

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5	277	Drops were setup with equal volume of protein and 0.2M MgCl2, 0.1M TRIS 8.5, 35% PEG 4000 (crystallization buffer) and suspended over 100ul of crystallization buffer., VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2	38.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.841	α = 90
b = 58.729	β = 90
c = 111.671	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	100	CCD	MARMOSAIC 225 mm CCD	MIRRORS	2012-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA		SLS	X06DA

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	2.056	41.84	98.9	0.116	9.6	6.1		17627

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	3B50	2.5	40.47	1.19	17627	491	98.5	0.215	0.213	0.22	0.255	0.26	26.13

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
f_dihedral_angle_d	13.65
f_angle_d	0.537
f_chiral_restr	0.021
f_bond_d	0.002
f_plane_restr	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2411
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	21

Software

Software
Software Name	Purpose
AMoRE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling

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.