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Crystal structure of human RIPK1 with Compound 1
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; 0.01 m NaAcetate pH 4.75; 0.12 M Na3Citrate; 0.28 M NH4I
Crystal Properties Matthews coefficient Solvent content 2.53 51.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.407 α = 90 b = 101.124 β = 90 c = 130.664 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 EIGER X 16M 2020-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9998 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 2.53 79.97 100 0.997 10.7 8.2 18320
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 2.53 79.97 0.408
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 2.53 79.97 18178 832 83.02 0.21707 0.21493 0.2169 0.26284 0.2625 RANDOM 76.691
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] -1.14 2.32 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.53 r_dihedral_angle_4_deg 14.06 r_dihedral_angle_3_deg 13.578 r_long_range_B_refined 9.008 r_long_range_B_other 9.007 r_mcangle_it 6.749 r_mcangle_other 6.747 r_scangle_other 6.482 r_dihedral_angle_1_deg 6.081 r_mcbond_other 4.365
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.53 r_dihedral_angle_4_deg 14.06 r_dihedral_angle_3_deg 13.578 r_long_range_B_refined 9.008 r_long_range_B_other 9.007 r_mcangle_it 6.749 r_mcangle_other 6.747 r_scangle_other 6.482 r_dihedral_angle_1_deg 6.081 r_mcbond_other 4.365 r_mcbond_it 4.364 r_scbond_it 4.262 r_scbond_other 4.261 r_angle_refined_deg 1.534 r_angle_other_deg 1.245 r_chiral_restr 0.086 r_bond_refined_d 0.011 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 4277 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 43
Software Software Software Name Purpose autoPROC data reduction XDS data reduction autoPROC data scaling Aimless data scaling REFMAC refinement