3HE7

Crystal structure of mouse CD1d-alpha-galactosylceramide with mouse Valpha14-Vbeta7 NKT TCR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HE6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529817% polyethylene glycol 10K, 0.1M ammonium acetate, 0.1M Bis Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
358.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.229α = 90
b = 81.913β = 90
c = 243.253γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102008-09-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.95667Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.85099.70.1320.13213.7729526295261161.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.9599.10.7070.7072.25.84192

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUT3HE62.850112804128041148099.650.226140.223680.27117RANDOM44.162
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]
0.950.74-1.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.532
r_dihedral_angle_3_deg16.983
r_dihedral_angle_4_deg16.185
r_dihedral_angle_1_deg5.476
r_angle_refined_deg1.029
r_scangle_it0.914
r_scbond_it0.545
r_mcangle_it0.403
r_nbtor_refined0.299
r_mcbond_it0.229
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.532
r_dihedral_angle_3_deg16.983
r_dihedral_angle_4_deg16.185
r_dihedral_angle_1_deg5.476
r_angle_refined_deg1.029
r_scangle_it0.914
r_scbond_it0.545
r_mcangle_it0.403
r_nbtor_refined0.299
r_mcbond_it0.229
r_nbd_refined0.184
r_symmetry_vdw_refined0.145
r_symmetry_hbond_refined0.12
r_xyhbond_nbd_refined0.118
r_chiral_restr0.065
r_bond_refined_d0.006
r_gen_planes_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6528
Nucleic Acid Atoms
Solvent Atoms45
Heterogen Atoms116

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling