1OD9 | pdb_00001od9

N-terminal of Sialoadhesin in complex with Me-a-9-N-benzoyl-amino-9-deoxy-Neu5Ac (BENZ compound)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QFO	DOMAIN A OF PDB ENTRY 1QFO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.6		1+1 DROP WITH 22.5 % (W/V) PEG 4000, 10 MM DTT, 0.18M AMMONIUM SULFATE, 0.09M SODIUM ACETATE PH 4.6,25MM BENZ COMPOUND

Crystal Properties
Matthews coefficient	Solvent content
2.54	52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.86	α = 90
b = 67.86	β = 90
c = 69.247	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	110	CCD	ADSC CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX9.6		SRS	PX9.6

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	2.1	20	99.9	0.11	23.4	11.8		9849		-1.5	18.1

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	2.1	2.17	99.8		0.72	2.2

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	DOMAIN A OF PDB ENTRY 1QFO	2.1	19.72	9667	512	98.3	0.209	0.209	0.253	RANDOM	39.1

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]
-2.64			-2.64		5.29

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25.5
c_scangle_it	6.82
c_scbond_it	5.8
c_mcangle_it	4.3
c_mcbond_it	3.58
c_angle_deg	1.3
c_improper_angle_d	0.85
c_bond_d	0.011
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	928
Nucleic Acid Atoms
Solvent Atoms	71
Heterogen Atoms	35

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing