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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 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 2.2 44.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.476 α = 90 b = 104.776 β = 90 c = 37.984 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 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 1.9 50 94.6 0.197 0.955 8.8 7.8 17604
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 1.9 1.93 0.35
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 1.904 42.289 17604 881 76.214 0.192 0.1901 0.199 0.2248 0.2308 25.169
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] 0.136 0.911 -1.047
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.715 r_dihedral_angle_3_deg 16.995 r_dihedral_angle_6_deg 14.369 r_dihedral_angle_1_deg 7.527 r_lrange_other 7.288 r_lrange_it 7.287 r_scangle_it 5.538 r_scangle_other 5.536 r_mcangle_it 3.725 r_mcangle_other 3.724
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.715 r_dihedral_angle_3_deg 16.995 r_dihedral_angle_6_deg 14.369 r_dihedral_angle_1_deg 7.527 r_lrange_other 7.288 r_lrange_it 7.287 r_scangle_it 5.538 r_scangle_other 5.536 r_mcangle_it 3.725 r_mcangle_other 3.724 r_scbond_it 3.391 r_scbond_other 3.39 r_mcbond_it 2.301 r_mcbond_other 2.3 r_angle_refined_deg 1.752 r_angle_other_deg 0.607 r_symmetry_xyhbond_nbd_refined 0.279 r_chiral_restr 0.278 r_nbd_refined 0.221 r_symmetry_nbd_other 0.202 r_nbd_other 0.198 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.174 r_symmetry_nbd_refined 0.139 r_symmetry_nbtor_other 0.084 r_chiral_restr_other 0.035 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_symmetry_xyhbond_nbd_other 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2210 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing