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Structure of Abl kinase in complex with imatinib and GNF-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OPJ PDB entry 1OPJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 277 0.1 M MES pH 5.6, 0.2 M MgCl2, 18 % PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.54 51.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.07 α = 72.82 b = 65.268 β = 80.25 c = 66.259 γ = 84.86
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 2008-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0016 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.74 62.5 95.3 0.052 0.045 16.5 3.9 64929 64929 31.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.74 1.8 86.2 0.45 0.382 3.4 3.6
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 1OPJ 1.74 38.95 61682 61682 3247 95.39 0.20062 0.20062 0.19899 0.1963 0.23117 0.2276 RANDOM 33.307
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] -0.69 0.03 0.49 0.3 -0.43 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.015 r_dihedral_angle_4_deg 14.107 r_dihedral_angle_3_deg 12.949 r_dihedral_angle_1_deg 5.46 r_scangle_it 3.273 r_scbond_it 2.165 r_mcangle_it 1.91 r_angle_refined_deg 1.176 r_mcbond_it 1.043 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.015 r_dihedral_angle_4_deg 14.107 r_dihedral_angle_3_deg 12.949 r_dihedral_angle_1_deg 5.46 r_scangle_it 3.273 r_scbond_it 2.165 r_mcangle_it 1.91 r_angle_refined_deg 1.176 r_mcbond_it 1.043 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4620 Nucleic Acid Atoms Solvent Atoms 429 Heterogen Atoms 129
Software Software Software Name Purpose MAR345 data collection REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing