Experiment: 3SDD

 3SDD

Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-beta-lactosylceramide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629316% PEG 6000, 0.1M Sodium citrate, pH 6.0, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.3663.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.469α = 90
b = 94.469β = 90
c = 291.063γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray213CCDADSC QUANTUM 315rmirrors2011-03-10SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.95370Australian SynchrotronMX2

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
12.989.85599.90.1110.10213.26.83029430294
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)
12.93.061000.8180.81817.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT389.8527300137199.70.2610.2580.318random79.05
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]
0.170.17-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.58
r_dihedral_angle_4_deg15.66
r_dihedral_angle_3_deg14.58
r_dihedral_angle_1_deg4.746
r_angle_refined_deg0.927
r_mcangle_it0.465
r_scangle_it0.336
r_mcbond_it0.258
r_scbond_it0.181
r_chiral_restr0.057
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6495
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms122

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction