7FI8

Crystal structure of human MICA mutants in complex with natural killer cell receptor NKG2D


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION72930.6 M Potassium sodium tartrate tetrahydrate, 0.1 M Tris pH 8.7, 1% Glycerol
Crystal Properties
Matthews coefficientSolvent content
2.9458.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.481α = 90
b = 121.481β = 90
c = 102.063γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2021-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U10.97915SSRFBL18U1

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
12.819.97199.70.2510.2560.050.99815.725.719323
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)
12.82.9599.72.4582.5060.4810.67426.5

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 REPLACEMENTTHROUGHOUT1hyr2.819.9711835794899.490.20750.20430.2669RANDOM73.028
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]
-3.94-3.947.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.378
r_dihedral_angle_3_deg20.416
r_dihedral_angle_4_deg19.795
r_dihedral_angle_1_deg8.512
r_angle_refined_deg1.689
r_angle_other_deg1.234
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.378
r_dihedral_angle_3_deg20.416
r_dihedral_angle_4_deg19.795
r_dihedral_angle_1_deg8.512
r_angle_refined_deg1.689
r_angle_other_deg1.234
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4139
Nucleic Acid Atoms
Solvent Atoms11
Heterogen Atoms

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing