7ZT9

Structure of E8 TCR in complex in human MR1 bound to 4FBA


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M HEPES pH 7.5, 20% PEG 4000, 15% Glycerol
Crystal Properties
Matthews coefficientSolvent content
2.5551.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.54α = 90
b = 96.24β = 90
c = 117.25γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2019-11-29MSINGLE 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
12.1358.621000.1090.1130.0290.99915.314.956786
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)
12.132.171002.6562.7460.6920.468115.5

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 REPLACEMENTTHROUGHOUT5U6Q2.1358.6253880283899.980.198280.195860.24367RANDOM57.594
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]
3.13-1.71-1.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.062
r_dihedral_angle_4_deg16.938
r_dihedral_angle_3_deg16.081
r_dihedral_angle_1_deg8.269
r_long_range_B_refined8.034
r_long_range_B_other8.033
r_scangle_other6.862
r_mcangle_it5.68
r_mcangle_other5.679
r_scbond_it5.142
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.062
r_dihedral_angle_4_deg16.938
r_dihedral_angle_3_deg16.081
r_dihedral_angle_1_deg8.269
r_long_range_B_refined8.034
r_long_range_B_other8.033
r_scangle_other6.862
r_mcangle_it5.68
r_mcangle_other5.679
r_scbond_it5.142
r_scbond_other5.141
r_mcbond_it4.381
r_mcbond_other4.381
r_angle_refined_deg1.59
r_angle_other_deg1.234
r_chiral_restr0.065
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.002
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 Atoms6395
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing