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Human ABL kinase in complex with nilotinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Unpublished structure of Abl complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 10.5 % PEG 5000 MME, 0.1 M MES pH 5.5, 0.05 ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.68 54.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.926 α = 90 b = 118.088 β = 90 c = 123.683 γ = 90
Symmetry Space Group P 21 21 21
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 MAR CCD 165 mm 2004-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00033 SLS X06SA
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 2.2 40 98.58 0.056 7.53 68942 68942
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) 2.2 2.28 97.1 0.401 6.25 6728
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(Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT Unpublished structure of Abl complex 2.21 40 65406 65406 3477 98.58 0.19965 0.19965 0.19744 0.2181 0.24186 0.2614 RANDOM 46.122
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] 0.02 0.58 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.392 r_dihedral_angle_4_deg 15.827 r_dihedral_angle_3_deg 15.245 r_dihedral_angle_1_deg 6.544 r_scangle_it 3.245 r_scbond_it 2.297 r_mcangle_it 1.664 r_angle_refined_deg 1.594 r_mcbond_it 1.217 r_angle_other_deg 1.035
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.392 r_dihedral_angle_4_deg 15.827 r_dihedral_angle_3_deg 15.245 r_dihedral_angle_1_deg 6.544 r_scangle_it 3.245 r_scbond_it 2.297 r_mcangle_it 1.664 r_angle_refined_deg 1.594 r_mcbond_it 1.217 r_angle_other_deg 1.035 r_symmetry_vdw_other 0.256 r_symmetry_hbond_refined 0.24 r_mcbond_other 0.236 r_symmetry_vdw_refined 0.233 r_nbd_refined 0.215 r_nbd_other 0.19 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.092 r_nbtor_other 0.092 r_bond_refined_d 0.019 r_gen_planes_other 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8274 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 156
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing