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Src kinase in complex with a quinazoline inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other In House
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 288 50 mM PIPES pH 6.5, 10 mM DTT, 100 mM sodium chloride and 4 to 9% PEG4000 (w/v), VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.584947 52.416824
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.806 α = 90 b = 72.467 β = 90 c = 171.566 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 ADSC QUANTUM 4 toroidal focusing mirror 2003-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 1.5418 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 49.8 95.49 0.083 0.115 3.4 29365 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 97.2 0.586 0.788 3.3 4508
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 In House 2.2 47.67 1 29365 29365 1566 95.49 0.20686 0.20351 0.2156 0.27216 0.2782 RANDOM 34.121
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] 1.79 0.46 -2.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.339 r_dihedral_angle_4_deg 21.777 r_dihedral_angle_3_deg 17.139 r_dihedral_angle_1_deg 6.897 r_scangle_it 2.91 r_scbond_it 1.842 r_angle_refined_deg 1.444 r_mcangle_it 1.394 r_angle_other_deg 1.026 r_mcbond_it 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.339 r_dihedral_angle_4_deg 21.777 r_dihedral_angle_3_deg 17.139 r_dihedral_angle_1_deg 6.897 r_scangle_it 2.91 r_scbond_it 1.842 r_angle_refined_deg 1.444 r_mcangle_it 1.394 r_angle_other_deg 1.026 r_mcbond_it 0.84 r_symmetry_vdw_other 0.256 r_nbd_refined 0.203 r_symmetry_hbond_refined 0.196 r_nbtor_refined 0.187 r_nbd_other 0.186 r_xyhbond_nbd_refined 0.166 r_mcbond_other 0.144 r_nbtor_other 0.088 r_chiral_restr 0.081 r_symmetry_vdw_refined 0.077 r_xyhbond_nbd_other 0.035 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3581 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction AMoRE phasing