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Structure of the kinase domain of human RIPK2 in complex with ponatinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PPZ PDB ENTRY 3PPZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 16% PEG3350, 0.1M AMMONIUM CITRATE
Crystal Properties Matthews coefficient Solvent content 2.28 45.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.735 α = 90 b = 86.682 β = 90 c = 137.335 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 DECTRIS HYBRID PIXEL 2013-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.75 58.74 100 0.12 12.1 7.2 18905 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.9 100 1.03 2 7.4
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 3PPZ 2.75 54.06 17887 969 99.96 0.20263 0.20061 0.2009 0.24361 0.2416 RANDOM 60.534
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] 2.36 -0.57 -1.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.986 r_dihedral_angle_3_deg 16.05 r_dihedral_angle_4_deg 14.958 r_dihedral_angle_1_deg 5.974 r_mcangle_it 3.418 r_mcbond_it 1.953 r_mcbond_other 1.945 r_scbond_it 1.782 r_angle_refined_deg 1.295 r_angle_other_deg 0.948
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.986 r_dihedral_angle_3_deg 16.05 r_dihedral_angle_4_deg 14.958 r_dihedral_angle_1_deg 5.974 r_mcangle_it 3.418 r_mcbond_it 1.953 r_mcbond_other 1.945 r_scbond_it 1.782 r_angle_refined_deg 1.295 r_angle_other_deg 0.948 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.004 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4318 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing