6CW6

Structure of alpha-GC[8,18] bound by CD1d and in complex with the Va14Vb8.2 TCR


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP42958% Tacsimate pH 4.0 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.7354.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.641α = 90
b = 190.354β = 90
c = 150.785γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-05-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-10.979SSRLBL7-1

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
12.854099.80.1390.1590.0755.94.526851
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.852.91000.5590.6380.3010.7044.6

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 REPLACEMENTTHROUGHOUT2Q7Y2.8539.3225731109599.670.21020.20850.2504RANDOM39.953
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]
0.08-0.03-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.055
r_dihedral_angle_4_deg16.071
r_dihedral_angle_3_deg14.468
r_dihedral_angle_1_deg6.849
r_angle_refined_deg1.276
r_angle_other_deg1.029
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.055
r_dihedral_angle_4_deg16.071
r_dihedral_angle_3_deg14.468
r_dihedral_angle_1_deg6.849
r_angle_refined_deg1.276
r_angle_other_deg1.029
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6367
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms126

Software

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