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crystal structure of BM3.3 ScFV TCR in complex with PBM8-H-2KBM8 MHC class I molecule
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NAM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 12 % PEG 6000, 100 mM Hepes, pH 7.5, and 150 mM Magnesium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.54 65.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.523 α = 90 b = 102.523 β = 90 c = 198.381 γ = 90
Symmetry Space Group P 43 21 2
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 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 2.9 25 98.1 0.116 22488
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 2.9 3.06
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 1NAM 2.9 25 22488 1214 98.13 0.2272 0.22422 0.2136 0.28352 0.2678 RANDOM 23.829
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] 3.14 3.14 -6.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.186 r_dihedral_angle_4_deg 18.478 r_dihedral_angle_3_deg 16.581 r_scangle_it 3.626 r_scbond_it 2.686 r_dihedral_angle_1_deg 2.65 r_mcangle_it 2.607 r_mcbond_it 1.722 r_angle_refined_deg 1.269 r_nbtor_refined 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.186 r_dihedral_angle_4_deg 18.478 r_dihedral_angle_3_deg 16.581 r_scangle_it 3.626 r_scbond_it 2.686 r_dihedral_angle_1_deg 2.65 r_mcangle_it 2.607 r_mcbond_it 1.722 r_angle_refined_deg 1.269 r_nbtor_refined 0.326 r_symmetry_hbond_refined 0.309 r_symmetry_vdw_refined 0.277 r_nbd_refined 0.262 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 Atoms Number Protein Atoms 4982 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing