3F6J | pdb_00003f6j

F17a-G lectin domain with bound GlcNAc(beta1-3)Gal

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O9V	PDB ENTRY 1O9V chain A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	293	10%(v/v) 2-propanol, 20%(w/v) PEG 4000, 100mM HEPES, pH 7.5, vapor diffusion, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.801	α = 90
b = 42.801	β = 90
c = 284.628	γ = 120

Symmetry
Space Group	P 61 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	100	CCD	MAR CCD 165 mm	mirrors	2006-05-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8047	EMBL/DESY, HAMBURG	X11

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	1.75	50	94.4	0.126	16.88	16.3	15865	15865			17.199

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	1.75	1.86	90.9		0.399	4.5	8.7	1366

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1O9V chain A	1.75	32.87	14782	14782	927	94.06	0.193	0.193	0.191	0.1932	0.232	0.2363	RANDOM	17.004

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]
-0.58	-0.29		-0.58		0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.838
r_dihedral_angle_4_deg	14.39
r_dihedral_angle_3_deg	12.567
r_dihedral_angle_1_deg	6.573
r_scangle_it	2.527
r_scbond_it	1.737
r_angle_refined_deg	1.316
r_mcangle_it	1.23
r_mcbond_it	0.731
r_nbtor_refined	0.305
r_symmetry_vdw_refined	0.233
r_nbd_refined	0.198
r_symmetry_hbond_refined	0.162
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1237
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing