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Rational development of high-affinity T-cell receptor-like antibodies
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RZF PDB ENTRY 1RZF AND 2BNQ experimental model PDB 2BNQ PDB ENTRY 1RZF AND 2BNQ
Crystallization Crystal Properties Matthews coefficient Solvent content 2.75 55.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.601 α = 90 b = 111.841 β = 93.49 c = 124.715 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 210 2005-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.933 ESRF ID14-1
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 1.9 30 153950
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 PDB ENTRY 1RZF AND 2BNQ 1.9 25 146102 7717 99.69 0.20446 0.20196 0.199 0.2514 0.2468 RANDOM 33.75
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] -0.66 0.68 0.15 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.055 r_dihedral_angle_4_deg 18.188 r_dihedral_angle_3_deg 16.025 r_dihedral_angle_1_deg 6.872 r_scangle_it 3.661 r_scbond_it 2.436 r_mcangle_it 1.734 r_angle_refined_deg 1.57 r_mcbond_it 1.048 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.055 r_dihedral_angle_4_deg 18.188 r_dihedral_angle_3_deg 16.025 r_dihedral_angle_1_deg 6.872 r_scangle_it 3.661 r_scbond_it 2.436 r_mcangle_it 1.734 r_angle_refined_deg 1.57 r_mcbond_it 1.048 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.279 r_nbd_refined 0.222 r_symmetry_hbond_refined 0.192 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.119 r_bond_refined_d 0.014 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 12728 Nucleic Acid Atoms Solvent Atoms 1603 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling