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Crystal structure of the anti-phosphorylated peptide C7 scFv antibody with peptide bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8JOW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.2 M Ammonium sulfate, 30% Polyethylene glycol 4000, 20 mM Tris HCl, 20 mM NaCl, pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.37 63.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.61 α = 90 b = 126.61 β = 90 c = 82.36 γ = 120
Symmetry Space Group P 32 2 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 315r 2017-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 2.8 21.1 99.8 0.176 0.055 0.996 12.8 11.1 19037
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 2.8 2.95 1.03 0.321 0.807 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.8 21.1 19017 1971 99.691 0.309 0.3044 0.3067 0.3452 0.3469 44.864
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 -0.12 -0.24 0.778
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.371 r_dihedral_angle_6_deg 12.467 r_dihedral_angle_2_deg 10.979 r_dihedral_angle_1_deg 7.456 r_lrange_it 5.635 r_lrange_other 5.635 r_scangle_it 3.344 r_scangle_other 3.264 r_mcangle_it 3.171 r_mcangle_other 3.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.371 r_dihedral_angle_6_deg 12.467 r_dihedral_angle_2_deg 10.979 r_dihedral_angle_1_deg 7.456 r_lrange_it 5.635 r_lrange_other 5.635 r_scangle_it 3.344 r_scangle_other 3.264 r_mcangle_it 3.171 r_mcangle_other 3.171 r_scbond_it 2.092 r_scbond_other 1.976 r_mcbond_it 1.919 r_mcbond_other 1.918 r_angle_refined_deg 1.371 r_angle_other_deg 0.491 r_nbd_other 0.241 r_symmetry_nbd_other 0.207 r_nbd_refined 0.186 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.174 r_symmetry_xyhbond_nbd_refined 0.158 r_xyhbond_nbd_refined 0.157 r_symmetry_xyhbond_nbd_other 0.119 r_symmetry_nbtor_other 0.086 r_ncsr_local_group_1 0.085 r_chiral_restr 0.064 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3602 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing