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The 1.6 A crystal structure of human bruton's tyrosine kinase bound to a pyrrolopyrimidine-containing compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K2P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 30% Peg MME 5000,0.2M Ammonium Sulfate, 0.1M MES pH 6.5 , VAPOR DIFFUSION, SITTING DROP, temperature 277.0K
Crystal Properties Matthews coefficient Solvent content 2.2 44.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.497 α = 90 b = 104.306 β = 90 c = 38.039 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 93 IMAGE PLATE RIGAKU Varimax HR optics 2008-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-D 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.6 24.5 98.1 0.08 3.8 38206 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.66 98.5 0.363 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1K2P 1.6 21.93 36293 36291 1915 98.13 0.1946 0.19261 0.226 0.23168 0.2616 RANDOM 28.639
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.97 r_dihedral_angle_4_deg 14.041 r_dihedral_angle_3_deg 12.911 r_dihedral_angle_1_deg 5.471 r_mcbond_other 2.876 r_scangle_it 2.39 r_scbond_it 1.739 r_sphericity_free 1.677 r_rigid_bond_restr 1.661 r_sphericity_bonded 1.577
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.97 r_dihedral_angle_4_deg 14.041 r_dihedral_angle_3_deg 12.911 r_dihedral_angle_1_deg 5.471 r_mcbond_other 2.876 r_scangle_it 2.39 r_scbond_it 1.739 r_sphericity_free 1.677 r_rigid_bond_restr 1.661 r_sphericity_bonded 1.577 r_angle_other_deg 1.265 r_mcangle_it 1.179 r_angle_refined_deg 1.145 r_mcbond_it 0.977 r_nbtor_refined 0.309 r_nbd_other 0.297 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.198 r_xyhbond_nbd_refined 0.186 r_symmetry_hbond_refined 0.157 r_nbtor_other 0.089 r_chiral_restr 0.081 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.003 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2161 Nucleic Acid Atoms Solvent Atoms 495 Heterogen Atoms 28
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling