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RIP2 kinase catalytic domain complex with (5S,6S,8R)-2-(benzo[d]thiazol-5-yl)-6-hydroxy-4,5,6,7,8,9-hexahydro-5,8-methanopyrazolo[1,5-a][1,3]diazocine-3-carboxamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AR2 PDB entry 5AR2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 85 mM Tris, pH 7.5, 200 mM calcium chloride, 10% PEG400, 5% glycerol, in 24 well Linbro trays at 22 degrees C. Crystals were frozen directly from the tray using paraffin oil as a cryoprotectant.
Crystal Properties Matthews coefficient Solvent content 3.71 66.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.677 α = 90 b = 125.677 β = 90 c = 105.76 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD MARMOSAIC 300 mm CCD 2015-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.9 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.68 105.76 100 0.111 0.12 0.044 0.997 12 7.2 27463
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.68 2.83 100 0.654 0.705 0.261 0.852 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB entry 5AR2 2.68 75.85 26118 1312 99.94 0.1849 0.1831 0.1887 0.22 0.2211 RANDOM 65.189
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] 0.99 0.49 0.99 -3.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.975 r_dihedral_angle_4_deg 13.071 r_dihedral_angle_3_deg 12.34 r_dihedral_angle_1_deg 5.692 r_angle_refined_deg 1.391 r_angle_other_deg 0.951 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.975 r_dihedral_angle_4_deg 13.071 r_dihedral_angle_3_deg 12.34 r_dihedral_angle_1_deg 5.692 r_angle_refined_deg 1.391 r_angle_other_deg 0.951 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4444 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 51
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing