3R52

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3R50PDB entry 3R50

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.60.05 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 coefficientSolvent content
2.1542.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.28α = 90
b = 83.71β = 112.76
c = 65.06γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210mirrors2009-07-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13C10.97622NSRRCBL13C1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.130970.06416.283.1332438.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1893.50.2693.62.73172

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3R502.125.9832172321693.80.1880.1880.243RANDOM27.5
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]
-1.614.840.820.79
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d27.2
c_scangle_it3.14
c_mcangle_it2.7
c_scbond_it2.14
c_mcbond_it1.66
c_angle_deg1.5
c_improper_angle_d0.88
c_bond_d0.01
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d27.2
c_scangle_it3.14
c_mcangle_it2.7
c_scbond_it2.14
c_mcbond_it1.66
c_angle_deg1.5
c_improper_angle_d0.88
c_bond_d0.01
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 AtomsNumber
Protein Atoms4625
Nucleic Acid Atoms
Solvent Atoms473
Heterogen Atoms55

Software

Software
Software NamePurpose
ADSCdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing