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Structure of the mouse invariant NKT cell receptor Valpha14
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TCR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295 16% PEG 4000, 0.2 M magnesium acetate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.69 54.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.293 α = 90 b = 150.518 β = 117.04 c = 65.814 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 flat mirror 2006-01-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97976 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.85 50 93 0.04 21.6 2 90127 90127
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 82.5 0.327 2 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1TCR 1.85 37.35 89468 88132 1336 93.06 0.18009 0.17945 0.177 0.22262 0.22 RANDOM 35.322
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] -0.21 -0.14 0.38 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.316 r_dihedral_angle_4_deg 12.931 r_dihedral_angle_3_deg 12.314 r_scangle_it 5.266 r_dihedral_angle_1_deg 4.98 r_scbond_it 4.742 r_mcangle_it 4.222 r_mcbond_it 2.862 r_angle_refined_deg 1.519 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.316 r_dihedral_angle_4_deg 12.931 r_dihedral_angle_3_deg 12.314 r_scangle_it 5.266 r_dihedral_angle_1_deg 4.98 r_scbond_it 4.742 r_mcangle_it 4.222 r_mcbond_it 2.862 r_angle_refined_deg 1.519 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.247 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.202 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.107 r_bond_refined_d 0.012 r_gen_planes_refined 0.001 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 Atoms Number Protein Atoms 6589 Nucleic Acid Atoms Solvent Atoms 546 Heterogen Atoms 123
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction MOLREP phasing