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The crystal structure of human abl1 kinase domain in complex with ABL1-B5
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 3.12 60.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.603 α = 90 b = 133.37 β = 90 c = 56.554 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 100 CCD MARMOSAIC 225 mm CCD 2022-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97 SSRF BL19U1
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 2.25 66.69 99.1 0.992 1.31 7.4 60553 29.7515645732
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 2.25 2.3 0.992
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.25495806781 66.685 1.35017444663 38064 1252 99.8557149978 0.176724497406 0.175473497035 0.1775 0.213408196047 0.2146 41.9352380218
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 15.3815416336 f_angle_d 0.673704824271 f_chiral_restr 0.0260174080965 f_plane_restr 0.00238472280976 f_bond_d 0.00220098474118
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4176 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 64
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction XDS data scaling PHENIX phasing