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c-Src V281C bound to N-[3-({6-[(1E)-2-cyano-3-(methylamino)-3-oxoprop-1-en-1-yl]-7-(2-methoxyethyl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl}ethynyl)-4-methylphenyl]-3-(trifluoromethyl)benzamide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UQG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 100 mM MES pH 6, 8% PEG 3350, 10 mM NaOAc, 14% glycerol, 10 mM DTT
Crystal Properties Matthews coefficient Solvent content 3.02 59.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.813 α = 77.87 b = 63.857 β = 90.1 c = 75.625 γ = 89.83
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2016-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.8 73.94 86.6 0.176 0.209 0.111 0.987 5.7 3.3 16285
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.97 85.6 1.334 1.578 0.833 0.498 3.3 2595
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 3uqg 2.8 73.94 15434 827 86.49 0.2881 0.2857 0.2886 0.3339 0.3323 RANDOM 64.488
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] -0.61 0.24 -0.06 -2.41 1.23 3.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.574 r_dihedral_angle_3_deg 16.381 r_dihedral_angle_4_deg 15.435 r_dihedral_angle_1_deg 7.117 r_mcangle_it 6.592 r_mcbond_it 3.853 r_mcbond_other 3.852 r_angle_refined_deg 1.423 r_angle_other_deg 0.965 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.574 r_dihedral_angle_3_deg 16.381 r_dihedral_angle_4_deg 15.435 r_dihedral_angle_1_deg 7.117 r_mcangle_it 6.592 r_mcbond_it 3.853 r_mcbond_other 3.852 r_angle_refined_deg 1.423 r_angle_other_deg 0.965 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4128 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing