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Mutant H493A 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 1.9 36.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.055 α = 90 b = 45.551 β = 104.274 c = 46.006 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M 2020-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9763 ESRF ID23-1
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 1.93 45.55 96.3 0.99 6.9 8.4 8443 1
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 1.93 2.03 77.9 0.66 1.18
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 1.95 44.586 8311 403 99.844 0.207 0.2049 0.2126 0.2545 0.2615 31.846
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] 4.371 -3.49 -1.512 -0.958
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.694 r_dihedral_angle_4_deg 20.172 r_dihedral_angle_3_deg 19.221 r_dihedral_angle_1_deg 10.264 r_lrange_it 8.133 r_lrange_other 8.13 r_scangle_it 6.104 r_scangle_other 6.1 r_scbond_it 3.822 r_scbond_other 3.818
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.694 r_dihedral_angle_4_deg 20.172 r_dihedral_angle_3_deg 19.221 r_dihedral_angle_1_deg 10.264 r_lrange_it 8.133 r_lrange_other 8.13 r_scangle_it 6.104 r_scangle_other 6.1 r_scbond_it 3.822 r_scbond_other 3.818 r_mcangle_it 3.785 r_mcangle_other 3.782 r_mcbond_other 2.483 r_mcbond_it 2.481 r_angle_refined_deg 1.673 r_angle_other_deg 1.233 r_symmetry_xyhbond_nbd_refined 0.307 r_symmetry_nbd_refined 0.204 r_symmetry_nbd_other 0.199 r_xyhbond_nbd_refined 0.186 r_nbd_refined 0.184 r_nbd_other 0.179 r_nbtor_refined 0.176 r_ncsr_local_group_1 0.14 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.064 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1003 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing