5TW2

Structure of mouse CD1d with bound alpha-galactosylsphingamide JG168


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Q7Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP429520% PEG 4000, 8% Tacsimate
Crystal Properties
Matthews coefficientSolvent content
2.8156.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.203α = 90
b = 107.466β = 90
c = 109.55γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.15SSRLBL7-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.754099.70.0610.0690.03314.34.351068
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.811000.5090.8344.3

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 REPLACEMENTTHROUGHOUT2Q7Y1.7530.249952105099.720.20320.202830.22134RANDOM32.776
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.307
r_dihedral_angle_4_deg19.723
r_dihedral_angle_3_deg11.424
r_dihedral_angle_1_deg6.035
r_long_range_B_refined5.485
r_long_range_B_other5.255
r_scangle_other3.265
r_mcangle_other2.944
r_mcangle_it2.943
r_scbond_it1.968
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.307
r_dihedral_angle_4_deg19.723
r_dihedral_angle_3_deg11.424
r_dihedral_angle_1_deg6.035
r_long_range_B_refined5.485
r_long_range_B_other5.255
r_scangle_other3.265
r_mcangle_other2.944
r_mcangle_it2.943
r_scbond_it1.968
r_scbond_other1.965
r_mcbond_it1.743
r_mcbond_other1.728
r_angle_refined_deg1.329
r_angle_other_deg0.976
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.001
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 Atoms2930
Nucleic Acid Atoms
Solvent Atoms339
Heterogen Atoms116

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKLdata reduction