2APF

Crystal Structure of the A52V/S54N/K66E variant of the murine T cell receptor V beta 8.2 domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72982.0 M Sodium Malonate, 0.2 % dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.855.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.608α = 90
b = 74.708β = 90
c = 113.819γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2003-09-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.5862.575188311420124
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.581.6665

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.8301142011154963094.090.203270.200590.197410.26271RANDOM28.169
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]
-0.320.81-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.932
r_dihedral_angle_4_deg19.151
r_dihedral_angle_3_deg14.48
r_dihedral_angle_1_deg6.635
r_scangle_it3.391
r_scbond_it2.308
r_angle_refined_deg1.526
r_mcangle_it1.361
r_mcbond_it0.794
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.932
r_dihedral_angle_4_deg19.151
r_dihedral_angle_3_deg14.48
r_dihedral_angle_1_deg6.635
r_scangle_it3.391
r_scbond_it2.308
r_angle_refined_deg1.526
r_mcangle_it1.361
r_mcbond_it0.794
r_nbtor_refined0.306
r_nbd_refined0.29
r_symmetry_hbond_refined0.281
r_xyhbond_nbd_refined0.194
r_symmetry_vdw_refined0.192
r_chiral_restr0.09
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms860
Nucleic Acid Atoms
Solvent Atoms151
Heterogen Atoms7

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
d*TREKdata scaling
MOLREPphasing