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Mutant Y526A of 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 3.2 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 210.639 α = 90 b = 62.485 β = 90 c = 87.056 γ = 90
Symmetry Space Group P 21 21 2
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 2020-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96546 ESRF MASSIF-1
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 1.537 49.35 99.8 0.99 11.9 6.3 329963
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 1.54 1.63 98.7 0.31
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7NYK 1.537 49.35 171114 1798 99.932 0.138 0.1378 0.1796 0.19 37.594
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] -1.416 3.466 -2.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.582 r_dihedral_angle_4_deg 15.775 r_dihedral_angle_3_deg 15.729 r_scangle_it 10.672 r_scangle_other 10.671 r_scbond_it 9.23 r_scbond_other 9.229 r_dihedral_angle_1_deg 8.95 r_lrange_it 8.475 r_lrange_other 8.474
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.582 r_dihedral_angle_4_deg 15.775 r_dihedral_angle_3_deg 15.729 r_scangle_it 10.672 r_scangle_other 10.671 r_scbond_it 9.23 r_scbond_other 9.229 r_dihedral_angle_1_deg 8.95 r_lrange_it 8.475 r_lrange_other 8.474 r_mcangle_other 5.896 r_mcangle_it 5.894 r_rigid_bond_restr 5.518 r_mcbond_it 5.318 r_mcbond_other 5.268 r_angle_refined_deg 1.864 r_angle_other_deg 1.415 r_symmetry_nbd_refined 0.246 r_nbd_other 0.226 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.21 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.177 r_symmetry_xyhbond_nbd_refined 0.151 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.087 r_symmetry_xyhbond_nbd_other 0.036 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6057 Nucleic Acid Atoms Solvent Atoms 700 Heterogen Atoms 280
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing