3UJO | pdb_00003ujo

Galactose-specific seed lectin from Dolichos lablab in complex with adenine and galactose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BJQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	30% PEG 4K, 100mM Tris pH 8.5, 200mM Na-acetate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.78	α = 90
b = 89.78	β = 90
c = 123.89	γ = 120

Symmetry
Space Group	P 32

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 300 mm CCD		2010-10-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97	ESRF	BM14

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	123.92	99.8	0.106	7.8	6.1		75331			26.7

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	2.11	98.8		0.52	2.4	5	10855

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1BJQ	2	42.2	71512	3754	99.63	0.20966	0.2075	0.2067	0.2495	0.2499	RANDOM	32.315

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]
-10.32			-10.32		20.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.061
r_dihedral_angle_4_deg	15.138
r_dihedral_angle_3_deg	14.18
r_dihedral_angle_1_deg	5.264
r_angle_refined_deg	0.915
r_scangle_it	0.547
r_scbond_it	0.364
r_mcangle_it	0.358
r_mcbond_it	0.201
r_chiral_restr	0.059
r_bond_refined_d	0.006
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7661
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms	130

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling