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The crystal structure of human abl1 kinase domain in complex with abl1-B-EBA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7W7Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.5M (NH4)2 SO4, 0.1M HEPES (PH 7.0) and 4% v/v 1,3-Propanediol.
Crystal Properties Matthews coefficient Solvent content 3.11 60.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.5018 α = 90 b = 104.976 β = 90 c = 132.487 γ = 90
Symmetry Space Group P 2 21 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 MARMOSAIC 225 mm CCD 2022-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.12 52.25 99.94 0.996 9.3 13.3 46218
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.196 0.64
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7W7Y 2.4501342407 42.988490614 1.33784226734 29696 1997 99.9192462988 0.205814881714 0.203775710345 0.2079 0.234153850318 0.2357 39.8427698956
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.4837098082 f_angle_d 0.683560507494 f_chiral_restr 0.0263211635032 f_bond_d 0.00316835911397 f_plane_restr 0.00279036033654
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4246 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction xia2 data scaling PHENIX phasing Coot model building