4DDN

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 DROP7298A drop containing 0.2 M sodium formate, 20% w/v Polyethylene glycol 3,350 against a reservoir of 0.4 M sodium formate, 40% w/v Polyethylene glycol 3,350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1442.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.075α = 90
b = 83.931β = 90
c = 86.129γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210mirrors2011-07-11MSINGLE 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
11.9301000.07329.97.3478496.4
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)
11.91.971000.3037.67.44705

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 3R501.926.0846397231997.60.1860.1860.228RANDOM20.4
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]
1.483.1-4.57
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d27.3
c_scangle_it2.95
c_mcangle_it2.14
c_scbond_it2.12
c_angle_deg1.9
c_mcbond_it1.43
c_improper_angle_d1.13
c_bond_d0.016
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d27.3
c_scangle_it2.95
c_mcangle_it2.14
c_scbond_it2.12
c_angle_deg1.9
c_mcbond_it1.43
c_improper_angle_d1.13
c_bond_d0.016
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 Atoms4668
Nucleic Acid Atoms
Solvent Atoms290
Heterogen Atoms52

Software

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