2NMO

Crystal structure of human galectin-3 carbohydrate-recognition domain at 1.35 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1A3KPDB ENTRY 1A3K

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729331% PEG 6000, 100mM MgCl2, 8mM beta mercaptoethanol, 100mM Tris-HCL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0740.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.315α = 90
b = 57.602β = 90
c = 62.22γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

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
11.3542.2697.60.0389.73.728612
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)
11.351.4287.30.1864.9

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1A3K1.3531.3627116145997.280.170220.169480.18441RANDOM12.931
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]
0.29-0.19-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.369
r_dihedral_angle_3_deg11.046
r_dihedral_angle_4_deg9.198
r_dihedral_angle_1_deg6.797
r_scangle_it4.15
r_scbond_it2.764
r_mcangle_it2.02
r_mcbond_it1.408
r_angle_refined_deg1.294
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.369
r_dihedral_angle_3_deg11.046
r_dihedral_angle_4_deg9.198
r_dihedral_angle_1_deg6.797
r_scangle_it4.15
r_scbond_it2.764
r_mcangle_it2.02
r_mcbond_it1.408
r_angle_refined_deg1.294
r_nbtor_refined0.31
r_nbd_refined0.192
r_symmetry_vdw_refined0.169
r_symmetry_hbond_refined0.131
r_chiral_restr0.089
r_xyhbond_nbd_refined0.079
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1108
Nucleic Acid Atoms
Solvent Atoms170
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing