5M62

Structure of the Mus musclus Langerin carbohydrate recognition domain in complex with glucose


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62930.1 M MES, pH 6.0, 30% (v/v) polyethylene glycol 600, 5% (w/v) polyethylene glycol 1000, and 10% (v/v) glycerol, 5% Glucose
Crystal Properties
Matthews coefficientSolvent content
3.5865.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.42α = 90
b = 144.42β = 90
c = 144.42γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.9763PETRA III, EMBL c/o DESYP14 (MX2)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)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
11.7501000.1140.116128.240.45492929.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.741001.7611.7830.853.241.1

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5K8Y1.745.675233025931000.144850.143850.16436RANDOM28.054
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]
-19.732.23-2.0110.17-39.829.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.755
r_dihedral_angle_4_deg16.591
r_dihedral_angle_3_deg12.216
r_dihedral_angle_1_deg6.686
r_long_range_B_refined3.844
r_long_range_B_other3.844
r_angle_refined_deg1.398
r_scangle_other1.345
r_mcangle_it1.065
r_mcangle_other1.064
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.755
r_dihedral_angle_4_deg16.591
r_dihedral_angle_3_deg12.216
r_dihedral_angle_1_deg6.686
r_long_range_B_refined3.844
r_long_range_B_other3.844
r_angle_refined_deg1.398
r_scangle_other1.345
r_mcangle_it1.065
r_mcangle_other1.064
r_angle_other_deg0.98
r_scbond_it0.856
r_scbond_other0.855
r_mcbond_it0.665
r_mcbond_other0.665
r_chiral_restr0.195
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2224
Nucleic Acid Atoms
Solvent Atoms276
Heterogen Atoms103

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing