6R0E

Structure of F11TCR in complex with DR1 MHC Class II presenting PKYVKQNTLKLAT


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FYT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION62910.1 M Na Cacodylate, 0.2 M NH4 SO4, 15 % PEG 8000
Crystal Properties
Matthews coefficientSolvent content
3.2462.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.28α = 90
b = 184.9β = 90
c = 50.2γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2015-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97623DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.9192.4699.90.0780.0840.0310.99914.17.29654339.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.911.9699.91.261.3540.4917.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1FYT1.9192.4596461476399.9050.2070.20550.233249.547
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]
-0.331-0.6791.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.264
r_dihedral_angle_1_deg18.656
r_dihedral_angle_4_deg17.013
r_dihedral_angle_3_deg15.772
r_dihedral_angle_other_3_deg11.667
r_lrange_other6.543
r_lrange_it6.542
r_scangle_it3.382
r_scangle_other3.382
r_mcangle_it2.556
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.264
r_dihedral_angle_1_deg18.656
r_dihedral_angle_4_deg17.013
r_dihedral_angle_3_deg15.772
r_dihedral_angle_other_3_deg11.667
r_lrange_other6.543
r_lrange_it6.542
r_scangle_it3.382
r_scangle_other3.382
r_mcangle_it2.556
r_mcangle_other2.555
r_scbond_it2.219
r_scbond_other2.219
r_angle_refined_deg1.709
r_mcbond_it1.613
r_mcbond_other1.613
r_angle_other_deg1.316
r_symmetry_nbd_refined0.265
r_nbd_other0.215
r_nbd_refined0.201
r_symmetry_nbd_other0.192
r_nbtor_refined0.168
r_symmetry_xyhbond_nbd_refined0.167
r_xyhbond_nbd_refined0.142
r_symmetry_nbtor_other0.085
r_chiral_restr0.077
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6567
Nucleic Acid Atoms
Solvent Atoms308
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
XDSdata scaling
PHASERphasing