2APT

Crystal Structure of the G17E/S54N/K66E/Q72H/E80V/L81S/T87S/G96V 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
3.159.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.423α = 90
b = 116.295β = 110.17
c = 34.769γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVmirrors2003-09-10MSINGLE 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
1234.492.3200081847624
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0565.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT234.4200081847696092.360.1770.1770.1750.21RANDOM39.722
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]
-0.11-0.53-0.960.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.369
r_dihedral_angle_3_deg18.699
r_dihedral_angle_4_deg12.668
r_dihedral_angle_1_deg6.81
r_scangle_it5.482
r_scbond_it3.581
r_mcangle_it2.201
r_angle_refined_deg1.879
r_mcbond_it1.271
r_nbtor_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.369
r_dihedral_angle_3_deg18.699
r_dihedral_angle_4_deg12.668
r_dihedral_angle_1_deg6.81
r_scangle_it5.482
r_scbond_it3.581
r_mcangle_it2.201
r_angle_refined_deg1.879
r_mcbond_it1.271
r_nbtor_refined0.316
r_nbd_refined0.279
r_xyhbond_nbd_refined0.181
r_chiral_restr0.148
r_symmetry_vdw_refined0.143
r_symmetry_hbond_refined0.126
r_bond_refined_d0.018
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1662
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms7

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata reduction
d*TREKdata scaling
MOLREPphasing