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X-ray crystal structure of ITK complexed with sunitinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SM2 PDB ENTRY 1SM2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 283 20% PEG3350, 0.2M AMMONIUM ACETATE, 0.1M BIS-TRIS, PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 283K
Crystal Properties Matthews coefficient Solvent content 2.16 43.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.479 α = 98.49 b = 52.053 β = 103.65 c = 66.106 γ = 92.84
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 ADSC QUANTUM 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.0 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.67 50 86.1 0.047 15.2 58467 53980 19.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.75 45.8 0.264 2.3 3350
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1SM2 1.67 32.02 49551 2680 86.12 0.20805 0.20665 0.2051 0.23391 0.2307 RANDOM 21.301
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] -0.51 -0.04 -0.33 -0.77 -1.05 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.087 r_dihedral_angle_4_deg 15.908 r_dihedral_angle_3_deg 12.987 r_dihedral_angle_1_deg 4.507 r_scangle_it 1.543 r_scbond_it 0.945 r_angle_refined_deg 0.913 r_mcangle_it 0.774 r_mcbond_it 0.446 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.087 r_dihedral_angle_4_deg 15.908 r_dihedral_angle_3_deg 12.987 r_dihedral_angle_1_deg 4.507 r_scangle_it 1.543 r_scbond_it 0.945 r_angle_refined_deg 0.913 r_mcangle_it 0.774 r_mcbond_it 0.446 r_nbtor_refined 0.298 r_nbd_refined 0.174 r_symmetry_vdw_refined 0.166 r_symmetry_hbond_refined 0.096 r_xyhbond_nbd_refined 0.091 r_chiral_restr 0.068 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3798 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 58
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling