2NN8

Crystal structure of human galectin-3 carbohydrate-recognition domain with lactose bound, 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
2.0941.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.371α = 90
b = 57.8β = 90
c = 62.603γ = 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 8.3.11.1159ALS8.3.1

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
11.3542.4998.30.03611.53.72918229182
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)
11.351.4289.90.213.4

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 1A3K1.3527.6227660148298.130.164760.164180.1749RANDOM13.881
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]
0.31-0.28-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.122
r_dihedral_angle_4_deg12.995
r_dihedral_angle_3_deg11.753
r_dihedral_angle_1_deg6.554
r_scangle_it4.118
r_scbond_it2.757
r_mcangle_it1.989
r_mcbond_it1.437
r_angle_refined_deg1.287
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.122
r_dihedral_angle_4_deg12.995
r_dihedral_angle_3_deg11.753
r_dihedral_angle_1_deg6.554
r_scangle_it4.118
r_scbond_it2.757
r_mcangle_it1.989
r_mcbond_it1.437
r_angle_refined_deg1.287
r_nbtor_refined0.31
r_nbd_refined0.193
r_symmetry_vdw_refined0.147
r_symmetry_hbond_refined0.109
r_xyhbond_nbd_refined0.093
r_chiral_restr0.089
r_bond_refined_d0.007
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1108
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing