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Crystal structure of human anaplastic lymphoma kinase in complex with a piperidine-carboxamide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other apo ALK (unpublished)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 27% PEG 5000 MME, 100 mM MES, 200 mM ammonium sulfate, 5 mM dithiothreitol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.08 40.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.612 α = 90 b = 104.819 β = 90.15 c = 57.817 γ = 90
Symmetry Space Group P 1 21 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 CCD MARMOSAIC 300 mm CCD 2009-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.03 50 98.5 0.048 11 2.3 39890 39292 -3 31.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.03 2.1 90.3 0.49 2 3591
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 (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R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT apo ALK (unpublished) 2.03 38.83 39732 39180 1972 98.61 0.2107 0.2082 0.2082 0.256 0.2542 RANDOM 34.4147
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] -0.6 -0.24 1.79 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.242 r_dihedral_angle_4_deg 16.24 r_dihedral_angle_3_deg 13.164 r_dihedral_angle_1_deg 5.236 r_scangle_it 2.197 r_mcangle_it 1.342 r_scbond_it 1.315 r_angle_refined_deg 1.027 r_mcbond_it 0.799 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.242 r_dihedral_angle_4_deg 16.24 r_dihedral_angle_3_deg 13.164 r_dihedral_angle_1_deg 5.236 r_scangle_it 2.197 r_mcangle_it 1.342 r_scbond_it 1.315 r_angle_refined_deg 1.027 r_mcbond_it 0.799 r_nbtor_refined 0.302 r_nbd_refined 0.182 r_symmetry_vdw_refined 0.174 r_symmetry_hbond_refined 0.126 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4499 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 72
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling EPMR phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling