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Drug resistant cSrc kinase domain in complex with covalent inhibitor PD168393
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HWP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 18% ethylene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.95 58.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.09 α = 78.49 b = 63.26 β = 88.33 c = 74.22 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray IMAGE PLATE MAR scanner 345 mm plate Multilayer Optic (Rigaku) 2006-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54170
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 2.48 52.63 93.6 0.095 0.095 8.5 2.2 26558 24859 42.1
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) 2.48 2.61 91.9 0.425 0.425 1.8 2.1 3559
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2HWP 2.48 52.63 24836 1268 93.56 0.225 0.221 0.2234 0.286 0.2876 RANDOM 32.425
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] 0.17 0.22 -0.33 -1.07 0.58 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.618 r_dihedral_angle_3_deg 19.401 r_dihedral_angle_4_deg 17.726 r_dihedral_angle_1_deg 12.686 r_scangle_it 3.702 r_scbond_it 2.359 r_angle_refined_deg 1.932 r_mcangle_it 1.759 r_mcbond_it 1.106 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.618 r_dihedral_angle_3_deg 19.401 r_dihedral_angle_4_deg 17.726 r_dihedral_angle_1_deg 12.686 r_scangle_it 3.702 r_scbond_it 2.359 r_angle_refined_deg 1.932 r_mcangle_it 1.759 r_mcbond_it 1.106 r_nbtor_refined 0.323 r_symmetry_hbond_refined 0.317 r_nbd_refined 0.248 r_symmetry_vdw_refined 0.237 r_xyhbond_nbd_refined 0.192 r_chiral_restr 0.125 r_bond_refined_d 0.019 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3895 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 46
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection