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Mutant V517A - SH3 domain of JNK-interacting Protein 1 (JIP1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NYK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 0.1 M HEPES pH 7.5, 1-5 % PEG 400, 2-2.5 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.12 α = 90 b = 84.254 β = 90 c = 98.315 γ = 90
Symmetry Space Group P 21 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 PIXEL DECTRIS PILATUS 6M 2020-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.45 63.976 94 0.99 7 12.5 45428
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.454 1.518 0.46 1.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7NYK 1.614 63.976 36326 1815 99.967 0.135 0.1314 0.1315 0.1976 0.1986 21.598
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] -0.658 1.586 -0.928
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.76 r_dihedral_angle_3_deg 15.267 r_dihedral_angle_4_deg 14.482 r_dihedral_angle_1_deg 9.433 r_scangle_it 6.761 r_scangle_other 6.761 r_lrange_other 5.653 r_lrange_it 5.652 r_scbond_other 5.538 r_scbond_it 5.535
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.76 r_dihedral_angle_3_deg 15.267 r_dihedral_angle_4_deg 14.482 r_dihedral_angle_1_deg 9.433 r_scangle_it 6.761 r_scangle_other 6.761 r_lrange_other 5.653 r_lrange_it 5.652 r_scbond_other 5.538 r_scbond_it 5.535 r_mcangle_it 2.922 r_mcangle_other 2.921 r_rigid_bond_restr 2.844 r_mcbond_it 2.381 r_mcbond_other 2.378 r_angle_refined_deg 1.68 r_angle_other_deg 1.373 r_nbd_refined 0.318 r_nbd_other 0.25 r_symmetry_nbd_other 0.227 r_symmetry_xyhbond_nbd_refined 0.2 r_xyhbond_nbd_refined 0.177 r_symmetry_nbd_refined 0.173 r_nbtor_refined 0.169 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2020 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing