☰ Navigation Tabs
The crystal structure of human abl1 kinase domain in complex with DP-987
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Abl kinase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.2 290 32% PEG 3000, 100MM TRIS PH 8.2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties Matthews coefficient Solvent content 2.15 42.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.783 α = 90 b = 116.915 β = 90 c = 78.837 γ = 90
Symmetry Space Group C 2 2 21
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 ADSC QUANTUM 315 2006-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL1-5 1.00002 SSRL BL1-5
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 2.3 20 100 0.098 15 12615 12613 34.3
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 (All) 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 Abl kinase 2.3 20 12615 12607 614 0.192 0.192 0.188 0.1894 0.281 0.2832 RANDOM 34.98
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] -2.24 1.67 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.955 r_dihedral_angle_4_deg 17.064 r_dihedral_angle_3_deg 16.674 r_dihedral_angle_1_deg 7.11 r_scangle_it 2.915 r_scbond_it 1.994 r_mcangle_it 1.641 r_angle_refined_deg 1.629 r_mcbond_it 1.003 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.955 r_dihedral_angle_4_deg 17.064 r_dihedral_angle_3_deg 16.674 r_dihedral_angle_1_deg 7.11 r_scangle_it 2.915 r_scbond_it 1.994 r_mcangle_it 1.641 r_angle_refined_deg 1.629 r_mcbond_it 1.003 r_nbtor_refined 0.308 r_nbd_refined 0.216 r_xyhbond_nbd_refined 0.179 r_symmetry_vdw_refined 0.158 r_symmetry_hbond_refined 0.157 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other 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 r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2185 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 34
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling