7ZT7

Structure of E8 TCR in complex in human MR1 bound to 5FSA


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 fluoride, 0.1 M Bis-Tris propane pH 8.5, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.0860.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.46α = 90
b = 104.42β = 90
c = 117.57γ = 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
11.8458.7999.980.0870.090.023115.514.798078
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)
11.841.8798.84.2214.4521.3770.3230.49.9

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 REPLACEMENTTHROUGHOUT5U6Q1.8458.7993125487199.90.209480.207140.25456RANDOM54.508
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]
13.71-4.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.326
r_dihedral_angle_3_deg14.77
r_dihedral_angle_4_deg14.024
r_long_range_B_refined7.842
r_long_range_B_other7.834
r_dihedral_angle_1_deg7.824
r_scangle_other5.908
r_mcangle_other4.481
r_mcangle_it4.48
r_scbond_it4.181
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.326
r_dihedral_angle_3_deg14.77
r_dihedral_angle_4_deg14.024
r_long_range_B_refined7.842
r_long_range_B_other7.834
r_dihedral_angle_1_deg7.824
r_scangle_other5.908
r_mcangle_other4.481
r_mcangle_it4.48
r_scbond_it4.181
r_scbond_other4.181
r_mcbond_it3.331
r_mcbond_other3.321
r_angle_refined_deg1.45
r_angle_other_deg1.244
r_chiral_restr0.062
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms6418
Nucleic Acid Atoms
Solvent Atoms345
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing