7ZT4

Structure of E8 TCR in complex with human MR1 bound to 6FP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5U6Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M Sodium iodide, 0.1 M Bis-Tris propane pH 8.5 and 20 % w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.1260.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.71α = 90
b = 104.39β = 90
c = 117.97γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2020-07-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
12.0258.991000.140.1450.0370.99913.115.274899
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)
12.022.051004.7864.9461.2340.2990.615.7

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 REPLACEMENTTHROUGHOUT5U6Q2.0258.9971062376299.970.2360.234310.26764RANDOM53.513
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]
-0.81-1.782.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.038
r_dihedral_angle_3_deg16.084
r_dihedral_angle_4_deg15.476
r_dihedral_angle_1_deg7.67
r_long_range_B_refined5.447
r_long_range_B_other5.435
r_mcangle_it1.622
r_mcangle_other1.621
r_angle_refined_deg1.476
r_scangle_other1.418
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.038
r_dihedral_angle_3_deg16.084
r_dihedral_angle_4_deg15.476
r_dihedral_angle_1_deg7.67
r_long_range_B_refined5.447
r_long_range_B_other5.435
r_mcangle_it1.622
r_mcangle_other1.621
r_angle_refined_deg1.476
r_scangle_other1.418
r_angle_other_deg1.215
r_mcbond_other0.956
r_mcbond_it0.955
r_scbond_other0.893
r_scbond_it0.892
r_chiral_restr0.062
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6369
Nucleic Acid Atoms
Solvent Atoms234
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing