3LEI | pdb_00003lei

Lectin Domain of Lectinolysin complexed with Fucose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52942M MgSO4, 100mM Tris, pH 8.5, vapor diffusion, hanging drop, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
3.2461.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.01α = 90
b = 67.01β = 90
c = 97.8γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVmirrors2008-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

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
11.942.6498.60.1249.68.6118008
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)
11.91.9787.70.42945.78

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3LEO1.942.641708591998.620.201830.199470.20.24690.24RANDOM23.803
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]
-0.11-0.110.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.005
r_dihedral_angle_3_deg15.56
r_dihedral_angle_4_deg15.016
r_dihedral_angle_1_deg6.892
r_scangle_it3.982
r_scbond_it2.561
r_mcangle_it1.598
r_angle_refined_deg1.448
r_mcbond_it0.916
r_chiral_restr0.125
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1114
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms13

Software

Software
Software NamePurpose
d*TREKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata reduction