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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 44.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.024 α = 90 b = 104.334 β = 90 c = 37.921 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 1.6 50 95.9 0.117 0.994 24.8 7.3 36963
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 1.601 1.643 0.783
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 1.601 42.285 36466 1810 94.673 0.154 0.1522 0.152 0.1855 0.1883 15.201
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] -0.096 0.364 -0.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.011 r_dihedral_angle_6_deg 15.542 r_dihedral_angle_3_deg 11.987 r_lrange_it 7.319 r_dihedral_angle_1_deg 7.134 r_lrange_other 6.827 r_scangle_it 4.7 r_scangle_other 4.699 r_mcangle_other 3.206 r_mcangle_it 3.203
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.011 r_dihedral_angle_6_deg 15.542 r_dihedral_angle_3_deg 11.987 r_lrange_it 7.319 r_dihedral_angle_1_deg 7.134 r_lrange_other 6.827 r_scangle_it 4.7 r_scangle_other 4.699 r_mcangle_other 3.206 r_mcangle_it 3.203 r_scbond_it 3.096 r_scbond_other 3.095 r_mcbond_it 2.016 r_mcbond_other 2.016 r_angle_refined_deg 1.942 r_dihedral_angle_other_2_deg 1.79 r_angle_other_deg 0.64 r_xyhbond_nbd_refined 0.227 r_nbd_refined 0.225 r_nbd_other 0.198 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.19 r_symmetry_nbd_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.172 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.038 r_bond_refined_d 0.011 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 428 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing