3KIH

The crystal structures of two fragments truncated from 5-bladed beta-propeller lectin, tachylectin-2 (Lib2-D2-15)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TL2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Microbatch under oil7298100mM HEPES, 0.2M magnesium chloride, 20% PEG 6000, pH 7, Microbatch under oil, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3748.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.566α = 90
b = 56.418β = 122.9
c = 86.306γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2009-04-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.495098.917718
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5490.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1TL22.4950170811681390598.430.236540.233110.29903RANDOM37.346
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]
-0.48-2.010.04-1.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.096
r_dihedral_angle_3_deg18.737
r_dihedral_angle_4_deg17.372
r_dihedral_angle_1_deg7.007
r_scangle_it2.162
r_angle_refined_deg1.52
r_scbond_it1.346
r_mcangle_it1.052
r_mcbond_it0.56
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.096
r_dihedral_angle_3_deg18.737
r_dihedral_angle_4_deg17.372
r_dihedral_angle_1_deg7.007
r_scangle_it2.162
r_angle_refined_deg1.52
r_scbond_it1.346
r_mcangle_it1.052
r_mcbond_it0.56
r_chiral_restr0.107
r_bond_refined_d0.012
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3675
Nucleic Acid Atoms
Solvent Atoms6
Heterogen Atoms60

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling