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Co-crystal structure of BTK kinase domain with non-covalent inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6X3N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 10% PEG 20000, 20% PEG MME 550, 0.03 M Sodium nitrate, 0.03 M disodium hydrogen phosphate, 0.03 M ammonium sulfate, and 0.1 M MES/Imidazole pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.99 38.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.184 α = 90 b = 104.171 β = 90 c = 37.842 γ = 90
Symmetry Space Group P 21 21 2
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 2022-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
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 2.5 50 92.4 0.945 8.6 4.3 7094
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 2.5 2.54 0.55
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.511 40.724 7093 321 76.359 0.275 0.2729 0.2744 0.3116 0.3185 50.538
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] 0.383 0.628 -1.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.332 r_lrange_it 16.575 r_lrange_other 16.575 r_dihedral_angle_2_deg 15.875 r_dihedral_angle_6_deg 15.754 r_scangle_it 7.288 r_scangle_other 7.286 r_mcangle_it 7.273 r_mcangle_other 7.271 r_dihedral_angle_1_deg 7.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.332 r_lrange_it 16.575 r_lrange_other 16.575 r_dihedral_angle_2_deg 15.875 r_dihedral_angle_6_deg 15.754 r_scangle_it 7.288 r_scangle_other 7.286 r_mcangle_it 7.273 r_mcangle_other 7.271 r_dihedral_angle_1_deg 7.098 r_scbond_it 4.333 r_scbond_other 4.332 r_mcbond_it 4.315 r_mcbond_other 4.313 r_angle_refined_deg 1.518 r_symmetry_xyhbond_nbd_refined 0.625 r_angle_other_deg 0.533 r_nbd_refined 0.253 r_symmetry_nbd_other 0.239 r_nbd_other 0.217 r_xyhbond_nbd_refined 0.211 r_nbtor_refined 0.198 r_symmetry_nbd_refined 0.137 r_dihedral_angle_other_2_deg 0.107 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_other 0.073 r_chiral_restr 0.069 r_chiral_restr_other 0.014 r_bond_refined_d 0.006 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 2198 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing