Experiment: 8B97

N-terminal beta-trefoil lectin domain of the Laccaria bicolor lectin in complex with N-acetyl-lactosamine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Y9F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	20% (w/v) PEG 6000, 0.1 M sodium acetate, pH 5.0, and 0.2 M ammonium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.472	α = 90
b = 61.026	β = 90
c = 44.549	γ = 90

Symmetry
Space Group	P 21 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	100	CCD	ADSC QUANTUM 315		2012-09-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.939	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	0.97	44.55	97	0.08	0.021	0.998	31.4	12.4		82583			4.94

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.97	1.02	80.1		0.071	0.962	10.9	9.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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	FREE R-VALUE	2y9f	0.97	44.55	1.35	82529	4125	96.82	0.1411	0.1405	0.1408	0.1524	0.1529	7.95

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	7.047
f_angle_d	1.145
f_chiral_restr	0.0801
f_plane_restr	0.0143
f_bond_d	0.0059

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1183
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms	130

Software

Software
Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing