2FIK

Structure of a microbial glycosphingolipid bound to mouse CD1d


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.527720 % Polyethylene glycol 4000, 0.1 M sodium citrate, 10% isopropanol, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K
Crystal Properties
Matthews coefficientSolvent content
2.8356.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.295α = 90
b = 107.661β = 90
c = 110.699γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-05-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.95369SSRLBL9-2

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
11.83799.90.07817.53.64780247802
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)
11.81.8599.90.7221.7

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2AKR1.834.144780046570123099.890.209150.20820.24253RANDOM25.285
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.626
r_dihedral_angle_4_deg22.177
r_dihedral_angle_3_deg15.029
r_dihedral_angle_1_deg6.969
r_scangle_it3.861
r_scbond_it2.485
r_mcangle_it1.804
r_angle_refined_deg1.568
r_mcbond_it1.099
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.626
r_dihedral_angle_4_deg22.177
r_dihedral_angle_3_deg15.029
r_dihedral_angle_1_deg6.969
r_scangle_it3.861
r_scbond_it2.485
r_mcangle_it1.804
r_angle_refined_deg1.568
r_mcbond_it1.099
r_nbtor_refined0.305
r_nbd_refined0.211
r_symmetry_hbond_refined0.207
r_symmetry_vdw_refined0.18
r_xyhbond_nbd_refined0.175
r_chiral_restr0.129
r_bond_refined_d0.014
r_gen_planes_refined0.007
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 Atoms2930
Nucleic Acid Atoms
Solvent Atoms379
Heterogen Atoms122

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing