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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
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.95 58.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.057 α = 90 b = 117.057 β = 90 c = 78.801 γ = 90
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 2005-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 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 2.3 30 44489 44489 428360
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 2.3 25 44459 2362 99.04 0.22628 0.22243 0.215 0.30231 0.294 RANDOM 44.399
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] 0.98 0.98 -1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.43 r_dihedral_angle_4_deg 26.367 r_dihedral_angle_3_deg 19.614 r_dihedral_angle_1_deg 12.773 r_scangle_it 4.029 r_scbond_it 2.731 r_mcangle_it 2.054 r_angle_refined_deg 2.034 r_mcbond_it 1.174 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.43 r_dihedral_angle_4_deg 26.367 r_dihedral_angle_3_deg 19.614 r_dihedral_angle_1_deg 12.773 r_scangle_it 4.029 r_scbond_it 2.731 r_mcangle_it 2.054 r_angle_refined_deg 2.034 r_mcbond_it 1.174 r_nbtor_refined 0.308 r_nbd_refined 0.246 r_symmetry_vdw_refined 0.228 r_xyhbond_nbd_refined 0.2 r_symmetry_hbond_refined 0.164 r_chiral_restr 0.142 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 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 6442 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling