☰ Navigation Tabs
Crystal structure of an allosteric inhibitor bound to human RIPK1 kinase domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other none
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 6 mM Gly3
29 %w/v PEG 3350
0,25 M NH4I
Crystal Properties Matthews coefficient Solvent content 2.2 44.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.582 α = 90 b = 98.129 β = 90 c = 127.126 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 2019-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.999999701977 SLS X10SA
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 2.29 77.68 96.9 0.99 19.02 4.63 123845
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.29 2.54 45
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.29 77.68 25527 1211 96.9 0.21947 0.21695 0.2751 0.2697 RANDOM 71.547
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] -0.58 0.73 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.818 r_dihedral_angle_4_deg 15.97 r_dihedral_angle_3_deg 13.616 r_long_range_B_other 8.631 r_long_range_B_refined 8.63 r_scangle_other 7.059 r_dihedral_angle_1_deg 6.448 r_mcangle_it 5.585 r_mcangle_other 5.585 r_scbond_it 5.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.818 r_dihedral_angle_4_deg 15.97 r_dihedral_angle_3_deg 13.616 r_long_range_B_other 8.631 r_long_range_B_refined 8.63 r_scangle_other 7.059 r_dihedral_angle_1_deg 6.448 r_mcangle_it 5.585 r_mcangle_other 5.585 r_scbond_it 5.153 r_scbond_other 5.143 r_mcbond_it 4.041 r_mcbond_other 4.035 r_angle_refined_deg 1.694 r_angle_other_deg 1.279 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.003 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4143 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 86
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PHASER phasing