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Crystal structure of BTK kinase domain complexed with 2-[8-fluoro-2-[2-(hydroxymethyl)-3-[1-methyl-5-[[5-(4-methylpiperazin-1-yl)-2-pyridyl]amino]-6-oxo-3-pyridyl]phenyl]-1-oxo-3,4-dihydroisoquinolin-6-yl]-2-methyl-propanenitrile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OTR PDB ENTRY 4OTR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 33% PEG3350, 0.1 M HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.937 α = 90 b = 106.339 β = 90 c = 38.429 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 CCD MARMOSAIC 325 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 2.5 42.76 88.84 0.141 5.6 3.4 9101 38.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.565 63.66 0.459 1.6 2
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 4OTR 2.5 42.76 9101 451 88.84 0.20306 0.19929 0.1993 0.28223 0.2792 RANDOM 33.479
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] 1.31 -0.28 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.527 r_dihedral_angle_4_deg 15.358 r_dihedral_angle_3_deg 14.114 r_dihedral_angle_1_deg 5.954 r_long_range_B_refined 4.321 r_mcangle_it 1.735 r_scbond_it 1.645 r_angle_refined_deg 1.32 r_mcbond_it 1.063 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.527 r_dihedral_angle_4_deg 15.358 r_dihedral_angle_3_deg 14.114 r_dihedral_angle_1_deg 5.954 r_long_range_B_refined 4.321 r_mcangle_it 1.735 r_scbond_it 1.645 r_angle_refined_deg 1.32 r_mcbond_it 1.063 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2139 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement CNS refinement ADSC data collection DENZO data reduction SCALEPACK data scaling CNS phasing