3CA0 | pdb_00003ca0

Sambucus nigra agglutinin II (SNA-II), hexagonal crystal form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AAI	chain B of ricin, PDN entry 2AAI

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
6.52	81.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.204	α = 90
b = 120.204	β = 90
c = 177.34	γ = 120

Symmetry
Space Group	P 64 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	ADSC QUANTUM 4		2002-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.937	ESRF	ID14-1

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	1.9	51.3	95.5	0.083	0.083	13.7	5	57308	57308			29.5

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	1.9	2	70		0.324	0.324	2.1	2.1	5977

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	MOLECULAR REPLACEMENT	THROUGHOUT	chain B of ricin, PDN entry 2AAI	1.95	20	52296	52296	2762	99.03	0.17259	0.17259	0.17146	0.18	0.19412	0.2	RANDOM	41.658

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]
0.78	0.39		0.78		-1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.937
r_dihedral_angle_4_deg	18.639
r_dihedral_angle_3_deg	12.748
r_dihedral_angle_1_deg	7.444
r_scangle_it	4.648
r_scbond_it	3.052
r_angle_refined_deg	1.907
r_mcangle_it	1.696
r_angle_other_deg	1.369
r_mcbond_it	1.323
r_symmetry_vdw_other	0.393
r_mcbond_other	0.31
r_nbd_other	0.216
r_nbd_refined	0.205
r_symmetry_hbond_refined	0.199
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.131
r_symmetry_vdw_refined	0.127
r_nbtor_other	0.113
r_bond_refined_d	0.021
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1980
Nucleic Acid Atoms
Solvent Atoms	335
Heterogen Atoms	209

Software

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