7ZT5

Structure of E8 TCR in complex in human MR1 bound to 3FSA


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 malonate dibasic monohydrate, 0.1 M Bis-Tris Propane pH 8.5, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.8757.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.97α = 90
b = 104.67β = 90
c = 117.7γ = 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
12.0958.8599.770.0910.0940.024114.91567006
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)
12.092.1397.044.975.1641.3830.3440.513.6

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 REPLACEMENTTHROUGHOUT5U6Q2.0958.8563556338499.660.227140.225070.26607RANDOM69.852
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]
-0.011.24-1.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.287
r_dihedral_angle_4_deg20.431
r_dihedral_angle_3_deg16.175
r_dihedral_angle_1_deg7.659
r_long_range_B_refined4.828
r_long_range_B_other4.821
r_scangle_other2.916
r_mcangle_it2.863
r_mcangle_other2.863
r_scbond_it1.849
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.287
r_dihedral_angle_4_deg20.431
r_dihedral_angle_3_deg16.175
r_dihedral_angle_1_deg7.659
r_long_range_B_refined4.828
r_long_range_B_other4.821
r_scangle_other2.916
r_mcangle_it2.863
r_mcangle_other2.863
r_scbond_it1.849
r_scbond_other1.846
r_mcbond_it1.816
r_mcbond_other1.815
r_angle_refined_deg1.479
r_angle_other_deg1.203
r_chiral_restr0.06
r_bond_refined_d0.009
r_gen_planes_refined0.007
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 Atoms6422
Nucleic Acid Atoms
Solvent Atoms77
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing