1ODA | pdb_00001oda

N-terminal of Sialoadhesin in complex with Me-a-9-N-(biphenyl-4-carbonyl)-amino-9-deoxy-Neu5Ac (BIP 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		5.6		ONE + ONE DROP WITH 30 % (W/V) PEG 4000, 10 MM DTT, 0.2M AMMONIUM ACETATE, 0.1M SODIUM CITRATE PH 5.6,2.5MM BIP COMPOUND

Crystal Properties
Matthews coefficient	Solvent content
2.54	52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.61	α = 90
b = 66.61	β = 90
c = 66.947	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	MARRESEARCH			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.2		SRS	PX14.2

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	3.3	20	89.7	0.192	9.2	5.5		2271

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	3.3	3.42	18.1		0.32	1.8

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	3.31	19.26	2154	195	87	0.217	0.217	0.284	RANDOM	35.1

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]
-16			-16		32

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	26
c_scangle_it	9.86
c_scbond_it	6.9
c_mcangle_it	5.86
c_mcbond_it	3.8
c_angle_deg	1.4
c_improper_angle_d	0.85
c_bond_d	0.008
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	914
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	35

Software

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