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003 Human T-Cell Receptor specific for HIV GAG epitope SLYNTVATL carried by Human Leukocyte Antigen HLA-A*0201
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GKZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 20% PEG 4K, 200mM Ammonium sulfate, 100mM Sodium cacodylate pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.29 46.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.15 α = 90 b = 81.17 β = 90.33 c = 64.9 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 PIXEL DECTRIS PILATUS3 6M 2013-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.29 50.69 94.9 16.1 3.7 106513 13.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 4GKZ 1.29 50.69 101171 5313 94.88 0.16957 0.16821 0.1763 0.19503 0.2017 RANDOM 18.944
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] 0.12 0.16 -0.27 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.488 r_dihedral_angle_4_deg 17.872 r_dihedral_angle_3_deg 13.175 r_dihedral_angle_1_deg 7.087 r_long_range_B_refined 6.648 r_long_range_B_other 6.647 r_scangle_other 2.957 r_angle_refined_deg 2.692 r_scbond_it 2.333 r_scbond_other 2.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.488 r_dihedral_angle_4_deg 17.872 r_dihedral_angle_3_deg 13.175 r_dihedral_angle_1_deg 7.087 r_long_range_B_refined 6.648 r_long_range_B_other 6.647 r_scangle_other 2.957 r_angle_refined_deg 2.692 r_scbond_it 2.333 r_scbond_other 2.333 r_mcangle_other 1.575 r_mcangle_it 1.573 r_angle_other_deg 1.376 r_mcbond_it 1.014 r_mcbond_other 1.001 r_chiral_restr 0.17 r_bond_refined_d 0.035 r_gen_planes_refined 0.015 r_bond_other_d 0.006 r_gen_planes_other 0.003 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 Atoms Number Protein Atoms 3497 Nucleic Acid Atoms Solvent Atoms 486 Heterogen Atoms 139
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data reduction Aimless data scaling PHASER phasing