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Crystal structure of the anti-phosphorylated peptide C7 Fab antibody with peptide bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8ZPU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.2 M Sodium chloride
19% Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.31 46.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.351 α = 112.536 b = 67.841 β = 104.989 c = 71.341 γ = 98.313
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2023-11-23 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 1.33 48.04 93.5 0.043 0.027 0.998 15.4 3.5 188006
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 1.33 1.35 66.6 0.463 0.296 0.781 2.2 3.3
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 1.33 48.04 188006 9562 93.531 0.138 0.1369 0.1464 0.1653 0.1741 18.556
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] 0.023 -0.166 0.022 -0.074 0.125 -0.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.525 r_lrange_it 12.13 r_lrange_other 11.929 r_dihedral_angle_3_deg 10.046 r_scangle_it 8.005 r_scangle_other 8.004 r_dihedral_angle_2_deg 7.496 r_mcangle_it 7.495 r_mcangle_other 7.495 r_dihedral_angle_1_deg 7.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.525 r_lrange_it 12.13 r_lrange_other 11.929 r_dihedral_angle_3_deg 10.046 r_scangle_it 8.005 r_scangle_other 8.004 r_dihedral_angle_2_deg 7.496 r_mcangle_it 7.495 r_mcangle_other 7.495 r_dihedral_angle_1_deg 7.146 r_scbond_it 5.482 r_scbond_other 5.481 r_mcbond_it 5.138 r_mcbond_other 5.136 r_rigid_bond_restr 3.054 r_angle_refined_deg 1.532 r_angle_other_deg 0.567 r_xyhbond_nbd_refined 0.233 r_nbd_refined 0.228 r_symmetry_nbd_other 0.207 r_nbd_other 0.201 r_nbtor_refined 0.174 r_symmetry_xyhbond_nbd_refined 0.167 r_symmetry_nbd_refined 0.09 r_symmetry_nbtor_other 0.089 r_chiral_restr 0.084 r_symmetry_xyhbond_nbd_other 0.053 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_chiral_restr_other 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6513 Nucleic Acid Atoms Solvent Atoms 848 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing