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Crystal structure of the scFv antibody 4B08 with epitope peptide (mutation N3A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YD3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 100 mM BIS-TRIS
1.8 M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.59 52.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.62 α = 90 b = 81.9 β = 90 c = 114.22 γ = 90
Symmetry Space Group P 2 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 CCD ADSC QUANTUM 270 2015-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.000 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.96 37.3 95.6 0.129 0.065 0.997 10 7.7 40361
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2.01 87.1 0.425 0.174 0.939 3.7 6.2
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 5YD3 1.96 37.3 38732 1584 95.37 0.20548 0.20342 0.2145 0.25789 0.2646 RANDOM 16.291
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] -2.91 10 -7.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.592 r_dihedral_angle_4_deg 19.597 r_dihedral_angle_3_deg 12.083 r_dihedral_angle_1_deg 6.906 r_long_range_B_refined 4.282 r_long_range_B_other 4.156 r_scangle_other 2.52 r_mcangle_it 1.818 r_mcangle_other 1.818 r_scbond_it 1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.592 r_dihedral_angle_4_deg 19.597 r_dihedral_angle_3_deg 12.083 r_dihedral_angle_1_deg 6.906 r_long_range_B_refined 4.282 r_long_range_B_other 4.156 r_scangle_other 2.52 r_mcangle_it 1.818 r_mcangle_other 1.818 r_scbond_it 1.68 r_scbond_other 1.586 r_angle_refined_deg 1.548 r_mcbond_it 1.122 r_mcbond_other 1.121 r_angle_other_deg 0.951 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 3845 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing