3C9Z | pdb_00003c9z

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Structure of SNA-II, hexagonal 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	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	1.35	64.55	99.6	0.075	0.075	14	4.6	66690	66690			16.2

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	1.35	1.39	99.7		0.395	0.395	2.3	3.3	4901

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	Structure of SNA-II, hexagonal crystal form	1.35	19.94	63280	63280	3366	99.51	0.16227	0.16227	0.1603	0.16	0.20049	0.2	RANDOM	24.002

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			-0.01		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.355
r_dihedral_angle_4_deg	18.681
r_dihedral_angle_3_deg	12.231
r_sphericity_free	10.775
r_sphericity_bonded	8.51
r_scangle_it	8.041
r_dihedral_angle_1_deg	7.268
r_scbond_it	6.29
r_mcangle_it	5.117
r_mcbond_it	4.204
r_rigid_bond_restr	4.083
r_angle_refined_deg	1.887
r_nbtor_refined	0.318
r_symmetry_vdw_refined	0.248
r_nbd_refined	0.219
r_symmetry_hbond_refined	0.203
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.143
r_bond_refined_d	0.02
r_gen_planes_refined	0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1979
Nucleic Acid Atoms
Solvent Atoms	245
Heterogen Atoms	142

Software

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