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Crystal structure of the JIP1-JIP2-SH3 heterodimer and the JIP2-JIP2-SH3 homodimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NYK JIP1-JIP1 SH3 dimer chain A,B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 Malonate 1.5 M
Crystal Properties Matthews coefficient Solvent content 2.8 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.47 α = 90 b = 68.47 β = 90 c = 177.259 γ = 120
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 EIGER X 9M 2021-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.96546 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.867 59.086 99.6 0.075 0.098 0.062 0.996 10.8 3.5 25670
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.867 1.899 100 0.55 0.644 0.332 0.76 2.7 3.6
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 1.867 59.086 25663 1283 99.577 0.15 0.1482 0.1593 0.1936 0.2024 23.922
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] 0.255 0.128 0.255 -0.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.801 r_dihedral_angle_3_deg 13.729 r_dihedral_angle_2_deg 13.022 r_dihedral_angle_1_deg 7.896 r_lrange_it 6.931 r_lrange_other 6.905 r_scangle_it 5.392 r_scangle_other 5.39 r_scbond_it 3.478 r_scbond_other 3.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.801 r_dihedral_angle_3_deg 13.729 r_dihedral_angle_2_deg 13.022 r_dihedral_angle_1_deg 7.896 r_lrange_it 6.931 r_lrange_other 6.905 r_scangle_it 5.392 r_scangle_other 5.39 r_scbond_it 3.478 r_scbond_other 3.476 r_mcangle_it 3.071 r_mcangle_other 3.07 r_mcbond_it 2.096 r_mcbond_other 2.096 r_angle_refined_deg 1.538 r_angle_other_deg 0.525 r_symmetry_nbd_refined 0.345 r_nbd_refined 0.222 r_symmetry_nbd_other 0.206 r_nbtor_refined 0.192 r_nbd_other 0.164 r_xyhbond_nbd_refined 0.146 r_symmetry_xyhbond_nbd_refined 0.127 r_symmetry_nbtor_other 0.091 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2038 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement AutoProcess data reduction STARANISO data scaling PHASER phasing