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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 2.2 44.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.505 α = 90 b = 104.801 β = 90 c = 37.938 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) 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 1.65 50 96.2 0.106 0.992 12.6 5.6 29004
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 1.65 1.68 0.614
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 1.655 42.302 29003 1470 83.273 0.167 0.1649 0.1775 0.2 0.2087 18.627
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] 0.321 0.142 -0.463
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.356 r_dihedral_angle_3_deg 14.155 r_dihedral_angle_2_deg 12.593 r_dihedral_angle_other_2_deg 8.662 r_lrange_it 7.464 r_lrange_other 7.34 r_dihedral_angle_1_deg 6.704 r_scangle_it 4.728 r_scangle_other 4.727 r_mcangle_other 3.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.356 r_dihedral_angle_3_deg 14.155 r_dihedral_angle_2_deg 12.593 r_dihedral_angle_other_2_deg 8.662 r_lrange_it 7.464 r_lrange_other 7.34 r_dihedral_angle_1_deg 6.704 r_scangle_it 4.728 r_scangle_other 4.727 r_mcangle_other 3.148 r_mcangle_it 3.144 r_scbond_it 2.984 r_scbond_other 2.983 r_mcbond_it 1.998 r_mcbond_other 1.982 r_angle_refined_deg 1.847 r_angle_other_deg 0.619 r_symmetry_nbd_refined 0.294 r_symmetry_xyhbond_nbd_refined 0.28 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.209 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.186 r_nbd_other 0.184 r_chiral_restr 0.09 r_symmetry_xyhbond_nbd_other 0.09 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2215 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing