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Structure based design of RIP1 kinase inhibitors
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.2 277 0.25 M ammonium iodide, 0.03 M glycyl-glycyl-glycine and polyethylene glycol (PEG) 3350 15-25%
Crystal Properties Matthews coefficient Solvent content 2.24 45.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.768 α = 90 b = 138.133 β = 96.08 c = 95.933 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 85 PIXEL DECTRIS PILATUS 6M 2016-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.9700 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.52 95.39 99 12.9 3.6 37759
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.52 2.58
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 2.52 95.39 37639 1976 98.95 0.24554 0.23625 0.2377 0.29643 0.3051 RANDOM 71.72
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] -3.85 1.04 -0.99 4.52
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 49.268 r_dihedral_angle_2_deg 35.55 r_sphericity_bonded 32.738 r_dihedral_angle_3_deg 15.993 r_dihedral_angle_4_deg 14.47 r_dihedral_angle_1_deg 5.435 r_long_range_B_refined 5.113 r_long_range_B_other 5.111 r_mcangle_it 4.881 r_mcangle_other 4.88
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 49.268 r_dihedral_angle_2_deg 35.55 r_sphericity_bonded 32.738 r_dihedral_angle_3_deg 15.993 r_dihedral_angle_4_deg 14.47 r_dihedral_angle_1_deg 5.435 r_long_range_B_refined 5.113 r_long_range_B_other 5.111 r_mcangle_it 4.881 r_mcangle_other 4.88 r_rigid_bond_restr 4.237 r_scangle_other 3.907 r_mcbond_it 3.617 r_mcbond_other 3.617 r_scbond_it 3.228 r_scbond_other 3.228 r_angle_other_deg 0.964 r_angle_refined_deg 0.946 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8471 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing