6CWB

Structure of alpha-GSA[8,4P] 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 DROP4.12950.06M Citric acid, 0.04M BIS-TRIS propane, 16% PEG 3350, pH 4.1
Crystal Properties
Matthews coefficientSolvent content
2.9858.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.31α = 90
b = 190.269β = 90
c = 151.018γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-03-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.00SSRLBL7-1

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
12.8595.1399.60.1730.1990.0976.64.226745
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)
12.852.9599.80.6740.7730.3730.6624.3

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 REPLACEMENTTHROUGHOUT2Q7Y2.8535.2225340138099.360.21820.21520.275RANDOM49.708
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]
-0.060.17-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.457
r_dihedral_angle_4_deg16.766
r_dihedral_angle_3_deg14.897
r_dihedral_angle_1_deg6.616
r_angle_refined_deg1.291
r_angle_other_deg1.088
r_chiral_restr0.072
r_bond_refined_d0.008
r_bond_other_d0.005
r_gen_planes_refined0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.457
r_dihedral_angle_4_deg16.766
r_dihedral_angle_3_deg14.897
r_dihedral_angle_1_deg6.616
r_angle_refined_deg1.291
r_angle_other_deg1.088
r_chiral_restr0.072
r_bond_refined_d0.008
r_bond_other_d0.005
r_gen_planes_refined0.004
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6299
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms129

Software

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