4HR6

Crystal structure of snake gourd (Trichosanthes anguina) seed lectin, a three chain homologue of type II RIPs


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729830% PEG 400, 80% ammonium sulfate, 10mM methyl D-galactose, 5mM mercaptoethanol , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
3.5865.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.081α = 90
b = 102.081β = 90
c = 271.64γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMAR scanner 345 mm plate2001-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1.0ELETTRA5.2R

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
12.253093.50.14416.78.340805
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)
12.252.3395.70.7513.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.2525.5240805190193.50.189080.187020.22873RANDOM48.826
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]
0.230.230.23-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.025
r_dihedral_angle_3_deg15.376
r_dihedral_angle_4_deg13.503
r_dihedral_angle_1_deg6.379
r_mcangle_it4.03
r_scbond_it3.011
r_mcbond_it2.623
r_mcbond_other2.623
r_angle_refined_deg1.226
r_angle_other_deg0.742
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.025
r_dihedral_angle_3_deg15.376
r_dihedral_angle_4_deg13.503
r_dihedral_angle_1_deg6.379
r_mcangle_it4.03
r_scbond_it3.011
r_mcbond_it2.623
r_mcbond_other2.623
r_angle_refined_deg1.226
r_angle_other_deg0.742
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3959
Nucleic Acid Atoms
Solvent Atoms178
Heterogen Atoms26

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling