3R52

Structure analysis of a wound-inducible lectin ipomoelin from sweet potato

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3R50	PDB entry 3R50

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6		0.05 M sodium acetate, 0.05 M cadmium chloride, 15% polyethylene glycol 400 (PEG 400) against a reservoir of 0.1 M sodium acetate, 0.1 M cadmium chloride, 30% PEG 400, pH 4.6, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.28	α = 90
b = 83.71	β = 112.76
c = 65.06	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 210	mirrors	2009-07-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13C1	0.97622	NSRRC	BL13C1

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	2.1	30	97	0.064	16.28	3.1		33243			8.5

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	2.1	2.18	93.5		0.269	3.6	2.7	3172

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3R50	2.1	25.98	32172	3216	93.8	0.188	0.188	0.243	RANDOM	27.5

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]
-1.61		4.84	0.82		0.79

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	27.2
c_scangle_it	3.14
c_mcangle_it	2.7
c_scbond_it	2.14
c_mcbond_it	1.66
c_angle_deg	1.5
c_improper_angle_d	0.88
c_bond_d	0.01
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4625
Nucleic Acid Atoms
Solvent Atoms	473
Heterogen Atoms	55

Software

Software
Software Name	Purpose
ADSC	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing