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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 2.21 44.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.874 α = 90 b = 104.541 β = 90 c = 37.961 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 2022-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.9794 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.4 50 97.7 0.042 0.994 53.2 9.9 55896
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 0.133 0.987
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 1.4 42.309 55890 2734 97.628 0.157 0.1559 0.1558 0.1724 0.1722 15.6
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] -0.002 0.108 -0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.666 r_dihedral_angle_6_deg 15.838 r_dihedral_angle_3_deg 12.101 r_lrange_it 8.197 r_lrange_other 7.814 r_dihedral_angle_1_deg 7.377 r_scangle_it 4.821 r_scangle_other 4.819 r_mcangle_other 3.43 r_mcangle_it 3.427
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.666 r_dihedral_angle_6_deg 15.838 r_dihedral_angle_3_deg 12.101 r_lrange_it 8.197 r_lrange_other 7.814 r_dihedral_angle_1_deg 7.377 r_scangle_it 4.821 r_scangle_other 4.819 r_mcangle_other 3.43 r_mcangle_it 3.427 r_scbond_it 3.197 r_scbond_other 3.196 r_mcbond_it 2.135 r_mcbond_other 2.133 r_angle_refined_deg 2.082 r_angle_other_deg 0.661 r_nbd_refined 0.234 r_xyhbond_nbd_refined 0.223 r_nbd_other 0.209 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.19 r_symmetry_xyhbond_nbd_refined 0.169 r_symmetry_nbd_refined 0.134 r_chiral_restr 0.1 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_other 0.078 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2227 Nucleic Acid Atoms Solvent Atoms 451 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling HKL2Map phasing