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The crystal structure of human abl1 T315I mutant kinase domain in complex with PH-ELV-1022
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QOH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 289 100 mM MES pH 6.5, 20 mM magnesium acetate, 25% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.01 38.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.869 α = 90 b = 39.342 β = 104.32 c = 75.455 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS 6M 2024-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.19499 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.1 36.5 97.8 0.171 0.072 0.994 5.7 6.5 15458
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 92.8 1.929 0.903 0.324 0.7 5.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.1 36.5 14682 758 97.29 0.21233 0.21059 0.2161 0.24659 0.2528 RANDOM 42.835
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] 0.04 -0.76 0.48 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.584 r_dihedral_angle_3_deg 14.098 r_dihedral_angle_1_deg 7.6 r_long_range_B_refined 6.744 r_long_range_B_other 6.707 r_scangle_other 3.199 r_mcangle_other 2.423 r_mcangle_it 2.42 r_scbond_it 1.884 r_scbond_other 1.883
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.584 r_dihedral_angle_3_deg 14.098 r_dihedral_angle_1_deg 7.6 r_long_range_B_refined 6.744 r_long_range_B_other 6.707 r_scangle_other 3.199 r_mcangle_other 2.423 r_mcangle_it 2.42 r_scbond_it 1.884 r_scbond_other 1.883 r_mcbond_it 1.442 r_mcbond_other 1.432 r_angle_refined_deg 1.301 r_angle_other_deg 0.448 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 2171 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction Aimless data scaling PHASER phasing PHENIX refinement