3UJQ | pdb_00003ujq

Galactose-specific lectin from Dolichos lablab in complex with 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 HCl, 200mM Mg-acetate , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.99	α = 90
b = 89.99	β = 90
c = 125.08	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	2.06	125.11	99.6	0.118	8.8	4		69408			33.3

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	2.06	2.18	98.3		0.307	4	3.8	10008

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	2.06	42.34	65893	3492	99.42	0.19895	0.1965	0.1964	0.2458	0.245	RANDOM	27.233

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]
-13.92			-13.92		27.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.557
r_dihedral_angle_3_deg	13.323
r_dihedral_angle_4_deg	12.025
r_dihedral_angle_1_deg	4.754
r_angle_refined_deg	0.838
r_scangle_it	0.294
r_mcangle_it	0.23
r_scbond_it	0.181
r_mcbond_it	0.128
r_chiral_restr	0.052
r_bond_refined_d	0.005
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7664
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	97

Software

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