3CAH | pdb_00003cah

Sambucus nigra aggutinin II. tetragonal crystal form- complexed to fucose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		SAMBUCUS NIGRA AGGLUTININ ii 6 TETRGONAL CRYSTAL FORM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	PROTEIN 16 MG/ML, AMMONIUM SULFATE 2.0 M, SODIUM ACETATE 100 mM, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.124	α = 90
b = 126.124	β = 90
c = 76.039	γ = 90

Symmetry
Space Group	I 41 2 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	MAR CCD 165 mm		2003-09-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.9795	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.55	34.68	98.8	0.044	0.044	32.4	5.7	43501	43501			15.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.64	92.9		0.095	0.095	11.5	3.2	5890

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	FOURIER SYNTHESIS	THROUGHOUT	SAMBUCUS NIGRA AGGLUTININ ii 6 TETRGONAL CRYSTAL FORM	1.55	20	41276	41276	2186	98.76	0.12485	0.12485	0.12265	0.14	0.16707	0.18	RANDOM	12.673

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]
-0.13			-0.13		0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.971
r_dihedral_angle_4_deg	19.88
r_dihedral_angle_3_deg	11.935
r_sphericity_free	11.584
r_dihedral_angle_1_deg	7.2
r_scangle_it	5.782
r_sphericity_bonded	4.584
r_scbond_it	4.286
r_mcangle_it	2.776
r_mcbond_it	2.261
r_rigid_bond_restr	2.124
r_angle_refined_deg	2.026
r_angle_other_deg	1.072
r_mcbond_other	0.845
r_symmetry_vdw_other	0.342
r_symmetry_vdw_refined	0.28
r_symmetry_hbond_refined	0.267
r_nbd_refined	0.233
r_xyhbond_nbd_refined	0.225
r_nbd_other	0.213
r_nbtor_refined	0.17
r_chiral_restr	0.16
r_nbtor_other	0.11
r_bond_refined_d	0.021
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1978
Nucleic Acid Atoms
Solvent Atoms	341
Heterogen Atoms	170

Software

Software
Software Name	Purpose
REFMAC	refinement
DNA	data collection
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing