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Crystal structure of human RIPK1 with Compound 22
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ITH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 20% (w/v) PEG3350; 6 mM Gly3; 0.22 M NH4I
Crystal Properties Matthews coefficient Solvent content 2.21 44.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.307 α = 90 b = 95.163 β = 90 c = 128.121 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 EIGER2 XE 16M 2020-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 1.0001 Diamond I03
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 2.32 76.4 99.6 0.998 16.5 7.9 25627
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 2.32 2.36 0.962
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 MOLECULAR REPLACEMENT THROUGHOUT 2.32 76.4 22093 1034 89.9 0.24247 0.23913 0.2382 0.31468 0.305 RANDOM 82.762
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] 1.72 3.63 -5.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.727 r_dihedral_angle_3_deg 13.788 r_dihedral_angle_4_deg 11.133 r_long_range_B_refined 9.727 r_long_range_B_other 9.725 r_mcangle_it 7.52 r_mcangle_other 7.519 r_scangle_other 7.427 r_dihedral_angle_1_deg 6.9 r_mcbond_other 5.245
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.727 r_dihedral_angle_3_deg 13.788 r_dihedral_angle_4_deg 11.133 r_long_range_B_refined 9.727 r_long_range_B_other 9.725 r_mcangle_it 7.52 r_mcangle_other 7.519 r_scangle_other 7.427 r_dihedral_angle_1_deg 6.9 r_mcbond_other 5.245 r_mcbond_it 5.244 r_scbond_it 5.175 r_scbond_other 5.174 r_angle_refined_deg 1.58 r_angle_other_deg 1.235 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 4359 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 50
Software Software Software Name Purpose autoPROC data reduction XDS data reduction autoPROC data scaling Aimless data scaling REFMAC refinement