6W4Z

Galectin-8N terminal domain in complex with Methyl 3-O-[3-O-benzyloxy]-malonyl-beta-D-galactopyranoside


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5T7S 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP298.150.1M sodium citrate dihydrate pH 5.6, 20% PEG 4000, 10% IPA
Crystal Properties
Matthews coefficientSolvent content
2.2344.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.391α = 90
b = 40.003β = 98.222
c = 70.324γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2019-03-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.9537Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.5946.3299.90.1160.9978.86.841190
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.591.6299.71.5380.9460.8056.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5T7S1.5946.3141186213999.910.1940.19250.225519.814
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]
-0.0010.001-0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.949
r_dihedral_angle_4_deg20.393
r_dihedral_angle_3_deg14.68
r_lrange_it7.551
r_lrange_other7.551
r_dihedral_angle_1_deg7.176
r_scangle_it4.561
r_scangle_other4.56
r_scbond_it3.023
r_scbond_other3.022
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.949
r_dihedral_angle_4_deg20.393
r_dihedral_angle_3_deg14.68
r_lrange_it7.551
r_lrange_other7.551
r_dihedral_angle_1_deg7.176
r_scangle_it4.561
r_scangle_other4.56
r_scbond_it3.023
r_scbond_other3.022
r_mcangle_other2.584
r_mcangle_it2.582
r_angle_refined_deg1.837
r_mcbond_it1.781
r_mcbond_other1.774
r_angle_other_deg1.405
r_chiral_restr_other1.169
r_nbd_other0.287
r_symmetry_nbd_refined0.285
r_symmetry_xyhbond_nbd_refined0.262
r_nbd_refined0.223
r_symmetry_nbd_other0.186
r_xyhbond_nbd_refined0.173
r_nbtor_refined0.168
r_chiral_restr0.081
r_symmetry_nbtor_other0.08
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2432
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing