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BTK kinase domain with inhibitor 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other not deposited inhouse model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 277 20% v/v PEG 20000 0.1M NaCl 0.1M Na MES pH 6.5 2.5 mM mM (S)-4-(8-amino-3-(1-(4-(dimethylamino)butanoyl)pyrrolidin-2-yl)imidazo[1,5-a]pyrazin-1-yl)-N-(thiazol-2-yl)benzamide 5.0 mM (R)-4-(8-amino-3-(1-(3-methyloxetane-3-carbonyl)piperidin-3-yl)imidazo[1,5-a]pyrazin-1-yl)-N-(4-(trifluoromethyl)pyridin-2-yl)benzamide
Crystal Properties Matthews coefficient Solvent content 2.23 44.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.262 α = 90 b = 71.475 β = 90.68 c = 103.056 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 IMAGE PLATE RIGAKU RAXIS IV 2010-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.8 36 94.7 0.064 11.2 3.4 48820
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 1.8 1.9 94.7 0.51 1.5 2.9
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 not deposited inhouse model 1.8 103.05 45481 3322 94.65 0.18232 0.17945 0.1867 0.22596 0.2317 RANDOM 23.103
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] -0.29 -0.19 0.09 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.682 r_dihedral_angle_3_deg 13.566 r_dihedral_angle_4_deg 13.256 r_dihedral_angle_1_deg 6.291 r_long_range_B_refined 5.386 r_long_range_B_other 5.386 r_scangle_other 1.945 r_angle_refined_deg 1.748 r_mcangle_it 1.54 r_mcangle_other 1.539
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.682 r_dihedral_angle_3_deg 13.566 r_dihedral_angle_4_deg 13.256 r_dihedral_angle_1_deg 6.291 r_long_range_B_refined 5.386 r_long_range_B_other 5.386 r_scangle_other 1.945 r_angle_refined_deg 1.748 r_mcangle_it 1.54 r_mcangle_other 1.539 r_angle_other_deg 1.317 r_scbond_it 1.191 r_scbond_other 1.191 r_mcbond_it 0.9 r_mcbond_other 0.897 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_gen_planes_other 0.006 r_bond_other_d 0.005 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 4171 Nucleic Acid Atoms Solvent Atoms 517 Heterogen Atoms 234
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing