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Tyrosine kinase AS - a common ancestor of Src and Abl bound to Gleevec
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CDS PDB ENTRY 4CDS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 291 10 MG/ML OF LYSINE MODIFIED (ETHYLATED) PROTEIN IN 30 MM TRIS PH 8.0, 500 MM NACL, 1 MM GLEEVEC, MIXED 1:1 WITH 200 MM AMMONIUM ACETATE, 100 MM SODIUM ACETATE TRIHYDRATE PH 4.6 AND 30% PEG 4000, HANGING DROP, MICRO SEEDING WITH INITIAL CRYSTALS FROM A 96 WELL PLATE SCREEN, INITIAL CRYSTALS GREW ON A DUST PARTICLE, 18C
Crystal Properties Matthews coefficient Solvent content 2.17 43.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.029 α = 90 b = 56.869 β = 116.62 c = 76.118 γ = 90
Symmetry Space Group I 1 2 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 ADSC QUANTUM 315 2014-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 ALS 8.2.2
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 2.05 42.36 93.1 0.04 10.1 2.5 15954 2
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 2.05 2.11 96.8 0.41 2 2.5
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 PDB ENTRY 4CDS 2.05 62.43 14124 886 87.13 0.19044 0.18728 0.1951 0.24159 0.2483 RANDOM 59.54
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] 0.15 2.67 -3.16 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.719 r_dihedral_angle_3_deg 16.286 r_dihedral_angle_4_deg 12.224 r_dihedral_angle_1_deg 6.263 r_mcangle_it 5.207 r_scbond_it 4.219 r_mcbond_it 3.585 r_mcbond_other 3.571 r_angle_refined_deg 1.42 r_angle_other_deg 0.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.719 r_dihedral_angle_3_deg 16.286 r_dihedral_angle_4_deg 12.224 r_dihedral_angle_1_deg 6.263 r_mcangle_it 5.207 r_scbond_it 4.219 r_mcbond_it 3.585 r_mcbond_other 3.571 r_angle_refined_deg 1.42 r_angle_other_deg 0.974 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_other 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1968 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing