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Kinase domain of cSrc in complex with Dasatinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OIQ PDB ENTRY 2OIQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 10% PEG 20000, 15% glycerol, 85 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3 59.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.19 α = 78.71 b = 63.69 β = 89.96 c = 74.58 γ = 90.28
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD MARRESEARCH Dynamically bendable mirror 2008-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99990 SLS X10SA
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 96.9 0.054 18.75 3.7 38645 37432 -3 34.39
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 2.2 2.3 96.6 0.145 9.7 3.69 4637
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 PDB ENTRY 2OIQ 2.2 35.05 38645 37431 936 100 0.207 0.206 0.2045 0.257 0.2534 RANDOM 30.597
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 -0.01 -0.12 0.85 -0.16 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.594 r_dihedral_angle_4_deg 17.338 r_dihedral_angle_3_deg 16.218 r_dihedral_angle_1_deg 6.115 r_scangle_it 3.319 r_scbond_it 2.157 r_angle_refined_deg 1.549 r_mcangle_it 1.453 r_mcbond_it 0.882 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.594 r_dihedral_angle_4_deg 17.338 r_dihedral_angle_3_deg 16.218 r_dihedral_angle_1_deg 6.115 r_scangle_it 3.319 r_scbond_it 2.157 r_angle_refined_deg 1.549 r_mcangle_it 1.453 r_mcbond_it 0.882 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.217 r_symmetry_hbond_refined 0.215 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4138 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 78
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling