2Y9F | pdb_00002y9f

High-resolution Structural Insights on the Sugar-recognition and Fusion Tag Properties of a Versatile b-Trefoil Lectin Domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1W3A	PDB ENTRY 1W3A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		12% (W/V) PEG 4000, 100 MM TRIS-HCL, PH 8.5, 150 MM SODIUM ACETATE

Crystal Properties
Matthews coefficient	Solvent content
1.74	30

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.58	α = 90
b = 59.54	β = 90
c = 61.62	γ = 90

Symmetry
Space Group	P 21 21 21

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 315r			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1		ESRF	ID23-1

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	1.47	34	99.5	0.07	16.9	6.3		22387		2	11.5

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	1.47	1.55	98.4		0.32	5.4	6

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 1W3A	1.47	30.16	21152	1138	99.13	0.1593	0.15753	0.17	0.19372	0.2	RANDOM	13.192

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]
-0.01			-0.04		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.717
r_dihedral_angle_4_deg	29.171
r_dihedral_angle_3_deg	12.725
r_dihedral_angle_1_deg	7.305
r_scangle_it	4.758
r_scbond_it	3.243
r_angle_refined_deg	2.315
r_mcangle_it	2.115
r_mcbond_it	1.339
r_chiral_restr	0.179
r_bond_refined_d	0.03
r_gen_planes_refined	0.018
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1212
Nucleic Acid Atoms
Solvent Atoms	252
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing