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The structure of human BTK kinase domain in complex with a covalent inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VGO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1M LiSO4, 0.1M citric acid pH 5.5, 6% PEG 10000
Crystal Properties Matthews coefficient Solvent content 2.82 56.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.59 α = 90 b = 53.6 β = 100.04 c = 101.635 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU 2016-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9795 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.64 50 99.3 4.4 6.6 18634
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.64 2.93
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5VGO 2.64 47.158 17575 898 97.88 0.26794 0.26497 0.2698 0.326 0.3273 RANDOM 70.373
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] -4.16 1.99 6.57 -2.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.548 r_dihedral_angle_3_deg 18.291 r_dihedral_angle_4_deg 14.033 r_long_range_B_refined 12.919 r_long_range_B_other 12.917 r_mcangle_it 8.869 r_mcangle_other 8.868 r_scangle_other 7.958 r_dihedral_angle_1_deg 7.904 r_mcbond_it 5.405
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.548 r_dihedral_angle_3_deg 18.291 r_dihedral_angle_4_deg 14.033 r_long_range_B_refined 12.919 r_long_range_B_other 12.917 r_mcangle_it 8.869 r_mcangle_other 8.868 r_scangle_other 7.958 r_dihedral_angle_1_deg 7.904 r_mcbond_it 5.405 r_mcbond_other 5.402 r_scbond_it 4.901 r_scbond_other 4.9 r_angle_refined_deg 1.537 r_angle_other_deg 1.054 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3758 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing