☰ Navigation Tabs
Crystal structure of RIPK1 with compound 36
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 25% (w/v) PEG3350; 6 mM Gly3; 0,3 M NaF; 0.28 M NH4I
Crystal Properties Matthews coefficient Solvent content 2.22 44.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.376 α = 90 b = 96.077 β = 90 c = 127.923 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 X 16M 2021-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0000 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 2.68 76.823 90.4 0.991 7.7 8.1 13048
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 2.68 2.89 0.471
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 2.68 76.82 12386 661 76.47 0.22874 0.22645 0.2281 0.27172 0.2719 RANDOM 47.736
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] -3.38 1.25 2.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.675 r_dihedral_angle_3_deg 16.641 r_dihedral_angle_4_deg 14.845 r_dihedral_angle_1_deg 6.986 r_long_range_B_refined 3.975 r_long_range_B_other 3.974 r_mcangle_it 2.257 r_mcangle_other 2.257 r_scangle_other 1.739 r_angle_refined_deg 1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.675 r_dihedral_angle_3_deg 16.641 r_dihedral_angle_4_deg 14.845 r_dihedral_angle_1_deg 6.986 r_long_range_B_refined 3.975 r_long_range_B_other 3.974 r_mcangle_it 2.257 r_mcangle_other 2.257 r_scangle_other 1.739 r_angle_refined_deg 1.39 r_mcbond_it 1.263 r_mcbond_other 1.263 r_angle_other_deg 1.089 r_scbond_it 0.993 r_scbond_other 0.989 r_chiral_restr 0.059 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 4326 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 51
Software Software Software Name Purpose autoPROC data reduction XDS data reduction autoPROC data scaling Aimless data scaling REFMAC refinement