6CWE

Structure of alpha-GSA[8,6P] 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 3QUZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29520% PEG 4000, 0.2M di-Ammonium tartrate
Crystal Properties
Matthews coefficientSolvent content
2.9758.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.18α = 90
b = 190.168β = 90
c = 150.965γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.979SSRLBL9-2

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
12.24099.40.0830.0940.0438.84.457216
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)
12.22.281000.6440.7330.3410.6964.3

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 REPLACEMENTTHROUGHOUT3QUZ2.24054364283199.170.20570.20410.2357RANDOM41.42
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_deg36.261
r_dihedral_angle_3_deg13.192
r_dihedral_angle_4_deg13.023
r_dihedral_angle_1_deg6.352
r_angle_refined_deg1.324
r_angle_other_deg0.938
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.261
r_dihedral_angle_3_deg13.192
r_dihedral_angle_4_deg13.023
r_dihedral_angle_1_deg6.352
r_angle_refined_deg1.324
r_angle_other_deg0.938
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6339
Nucleic Acid Atoms
Solvent Atoms266
Heterogen Atoms144

Software

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