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RIP2K kinase domain dimer with bound compound 37 (N399), a speific NOD1 pathway inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Compound 37, in powder form was solubilized in DMSO at 5 mM concentration. One aliquot of protein at 1.14 mg/ml was thawed and mixed with 50 microM inhibitor and kept on ice for 10 minutes. The complex was than concentrated to 3.8 mg/ml. solutions containing 3.8 mg/ml of protein-inhibitor complex equilibrated against 0.1 M citric acid and 0.8 M sodium formate at pH 5.
Crystal Properties Matthews coefficient Solvent content 2.34 47.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.824 α = 90 b = 90.75 β = 90 c = 137.976 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 PILATUS3 6M 2023-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9655 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.943 54.981 96.1 0.093 0.104 0.996 8 5.3 48396
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.943 1.976 95.5 2.848 3.171 0.393 0.4
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 FREE R-VALUE 1.943 54.981 48396 2454 93.84 0.222 0.2203 0.2297 0.2564 0.2652 57.567
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] -1.722 3.057 -1.336
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.671 r_dihedral_angle_3_deg 14.331 r_lrange_it 9.651 r_lrange_other 9.643 r_dihedral_angle_2_deg 9.276 r_scangle_it 6.832 r_scangle_other 6.831 r_mcangle_it 5.99 r_mcangle_other 5.989 r_dihedral_angle_1_deg 5.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.671 r_dihedral_angle_3_deg 14.331 r_lrange_it 9.651 r_lrange_other 9.643 r_dihedral_angle_2_deg 9.276 r_scangle_it 6.832 r_scangle_other 6.831 r_mcangle_it 5.99 r_mcangle_other 5.989 r_dihedral_angle_1_deg 5.912 r_scbond_it 4.17 r_scbond_other 4.169 r_mcbond_it 3.913 r_mcbond_other 3.913 r_angle_refined_deg 1.084 r_angle_other_deg 0.37 r_nbd_other 0.212 r_nbd_refined 0.209 r_symmetry_xyhbond_nbd_refined 0.195 r_symmetry_nbd_other 0.188 r_symmetry_nbd_refined 0.186 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.152 r_ncsr_local_group_1 0.106 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.055 r_symmetry_xyhbond_nbd_other 0.044 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4504 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling