6VB8

Crystal structure of a lectin from Canavalia brasiliensis seed (ConBr) complexed with indole-3-acetic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3JU9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52981.8 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M HEPES, pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.3948.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.806α = 90
b = 72.427β = 90
c = 99.272γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2017-05-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.458LNLSW01B-MX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.249.6998.30.0460.0480.013130.411.912527
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.3288.80.2120.2250.0730.9948.98.9

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 REPLACEMENTFREE R-VALUE3JU92.249.691186466098.210.20050.19850.2356RANDOM45.966
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]
-0.493.32-2.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.426
r_dihedral_angle_3_deg13.668
r_dihedral_angle_4_deg12.655
r_dihedral_angle_1_deg8.569
r_angle_refined_deg1.274
r_angle_other_deg1.169
r_chiral_restr0.044
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.426
r_dihedral_angle_3_deg13.668
r_dihedral_angle_4_deg12.655
r_dihedral_angle_1_deg8.569
r_angle_refined_deg1.274
r_angle_other_deg1.169
r_chiral_restr0.044
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1775
Nucleic Acid Atoms
Solvent Atoms44
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing
SCALAdata scaling
XDSdata reduction
MxCuBEdata collection