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The role of T cell receptor alpha genes in directing human MHC restriction
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZHK PDB entry 1ZHK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 277 17% PEG 3350, 100mM cacodylate, 200mM ammonium acetate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.6 51.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.155 α = 90 b = 82.095 β = 90 c = 109.894 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS 2005-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 0.9 APS 17-ID
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 1.9 65.79 35560
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.949 98.57
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 (All) 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 PDB entry 1ZHK 1.9 34.06 35560 1132 98.57 0.23352 0.23362 0.23231 0.3103 0.27464 0.3349 RANDOM 29.58
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] -0.24 -0.31 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.913 r_dihedral_angle_4_deg 21.228 r_dihedral_angle_3_deg 12.802 r_dihedral_angle_1_deg 5.535 r_scangle_it 1.63 r_angle_refined_deg 1.049 r_scbond_it 0.999 r_mcangle_it 0.711 r_mcbond_it 0.46 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.913 r_dihedral_angle_4_deg 21.228 r_dihedral_angle_3_deg 12.802 r_dihedral_angle_1_deg 5.535 r_scangle_it 1.63 r_angle_refined_deg 1.049 r_scbond_it 0.999 r_mcangle_it 0.711 r_mcbond_it 0.46 r_nbtor_refined 0.297 r_symmetry_vdw_refined 0.173 r_nbd_refined 0.169 r_symmetry_hbond_refined 0.153 r_xyhbond_nbd_refined 0.112 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 3173 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing