4U2A

Structure of a lectin from the seeds of Vatairea macrocarpa complexed with GalNAc


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP3.5293Citric acid buffer, ammonium sulphate
Crystal Properties
Matthews coefficientSolvent content
2.8857.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.262α = 90
b = 85.52β = 90
c = 129.416γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2012-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.872ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.7471.3599.20.1230.1244.15.532066
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)
11.741.8494.30.542.9

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 REPLACEMENTTHROUGHOUT1.7471.3532066161999.120.16310.16170.1882RANDOM14.795
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]
0.370.98-1.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.637
r_dihedral_angle_4_deg19.857
r_dihedral_angle_3_deg12.9
r_dihedral_angle_1_deg6.742
r_mcangle_it2.632
r_angle_refined_deg2.056
r_mcbond_it1.762
r_mcbond_other1.668
r_angle_other_deg0.889
r_chiral_restr0.126
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.637
r_dihedral_angle_4_deg19.857
r_dihedral_angle_3_deg12.9
r_dihedral_angle_1_deg6.742
r_mcangle_it2.632
r_angle_refined_deg2.056
r_mcbond_it1.762
r_mcbond_other1.668
r_angle_other_deg0.889
r_chiral_restr0.126
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1777
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement