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RIPK1 in complex with AZ"902
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Inhouse
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20 % PEG4000, 0.3 M NaCl, 0.1 M MES pH 6.5.
Crystal Properties Matthews coefficient Solvent content 2.06 40.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.084 α = 90 b = 96.491 β = 90 c = 129.002 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 200K 2022-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.976 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.25 77.27 85.6 0.109 0.119 0.046 9 6.7 24404
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.255 2.395 26.4 1.459 1.576 0.591 7
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 2.25 77.27 23243 1161 85.63 0.22118 0.21725 0.2273 0.29485 0.2933 RANDOM 71.063
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] 0.05 -0.1 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.585 r_dihedral_angle_3_deg 17.989 r_long_range_B_refined 12.295 r_long_range_B_other 12.292 r_scangle_other 9.552 r_mcangle_it 9.177 r_mcangle_other 9.176 r_dihedral_angle_1_deg 8.435 r_scbond_it 6.647 r_scbond_other 6.596
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.585 r_dihedral_angle_3_deg 17.989 r_long_range_B_refined 12.295 r_long_range_B_other 12.292 r_scangle_other 9.552 r_mcangle_it 9.177 r_mcangle_other 9.176 r_dihedral_angle_1_deg 8.435 r_scbond_it 6.647 r_scbond_other 6.596 r_mcbond_it 6.505 r_mcbond_other 6.503 r_angle_refined_deg 1.497 r_angle_other_deg 0.475 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 4113 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing