3MIT | pdb_00003mit

Structure of Banana lectin-alpha-D-mannose complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X1V	PDB ENTRY 1X1V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	ZINC ACETATE DIHYDRATE, SODIUM CACODYLATE, 1,6-HEXANEDIOL, , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.77	74.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.926	α = 90
b = 80.926	β = 90
c = 148.173	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH	MIRRORS	2005-07-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.54

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	2.32	30	98.4	0.077	16.4	4.7	25080	24663

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	2.32	2.4	98.4		0.489	3.3		2392

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	PDB ENTRY 1X1V	2.32	25.46	23385	1257	100	0.20541	0.2033	0.2	0.24628	0.23	RANDOM	48.204

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]
2.08	1.04		2.08		-3.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.22
r_dihedral_angle_3_deg	15.238
r_dihedral_angle_4_deg	10.111
r_dihedral_angle_1_deg	6.253
r_scangle_it	1.51
r_angle_refined_deg	1.192
r_scbond_it	0.949
r_mcangle_it	0.675
r_mcbond_it	0.396
r_nbtor_refined	0.309
r_nbd_refined	0.184
r_symmetry_vdw_refined	0.155
r_metal_ion_refined	0.15
r_xyhbond_nbd_refined	0.126
r_symmetry_hbond_refined	0.087
r_chiral_restr	0.075
r_symmetry_metal_ion_refined	0.06
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2017
Nucleic Acid Atoms
Solvent Atoms	209
Heterogen Atoms	114

Software

Software
Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling