6C69

Structure of glycolipid aGSA[12,6P] in complex with mouse CD1d


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP42958% Tacsimate, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.8156.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.162α = 90
b = 107.399β = 90
c = 109.917γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-06-16MSINGLE 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
11.9350970.0630.0720.0347.83.936708
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)
11.931.9796.70.4580.5270.2560.8423.8

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 REPLACEMENTTHROUGHOUT2Q7Y1.9375035539111996.430.20150.20050.2327RANDOM41.04
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.658
r_dihedral_angle_4_deg20.168
r_dihedral_angle_3_deg14.001
r_dihedral_angle_1_deg6.29
r_angle_refined_deg1.355
r_angle_other_deg0.852
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.658
r_dihedral_angle_4_deg20.168
r_dihedral_angle_3_deg14.001
r_dihedral_angle_1_deg6.29
r_angle_refined_deg1.355
r_angle_other_deg0.852
r_chiral_restr0.077
r_bond_refined_d0.008
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 Atoms2968
Nucleic Acid Atoms
Solvent Atoms221
Heterogen Atoms134

Software

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