2NMN

Crystal structure of human galectin-3 carbohydrate-recognising domain at 2.45 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
2.2144.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.341α = 90
b = 58.238β = 90
c = 63.731γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295CCDBRUKER SMART 6000MIRRORS2005-07-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEMACSCIENCE

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
12.455898.40.04811.43.75400
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)
2.452.5684.10.1874.6

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1A3K2.4542.995400513424197.920.166570.163320.23734RANDOM23.831
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]
0.02-0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.734
r_dihedral_angle_3_deg15.944
r_dihedral_angle_4_deg15.924
r_dihedral_angle_1_deg7.063
r_scangle_it4.373
r_scbond_it2.528
r_angle_refined_deg1.688
r_mcangle_it1.48
r_mcbond_it1.009
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.734
r_dihedral_angle_3_deg15.944
r_dihedral_angle_4_deg15.924
r_dihedral_angle_1_deg7.063
r_scangle_it4.373
r_scbond_it2.528
r_angle_refined_deg1.688
r_mcangle_it1.48
r_mcbond_it1.009
r_nbtor_refined0.317
r_nbd_refined0.208
r_symmetry_hbond_refined0.199
r_xyhbond_nbd_refined0.183
r_symmetry_vdw_refined0.169
r_chiral_restr0.102
r_bond_refined_d0.016
r_gen_planes_refined0.006
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 Atoms54
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata collection
SAINTdata reduction
LSCALEdata scaling
AMoREphasing