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c-Src V281C kinase domain in complex with Rao-IV-151
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, 3% glycerol, 10 mM DTT, 10 mM NaOAc
Crystal Properties Matthews coefficient Solvent content 3.28 62.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.819 α = 77.94 b = 64.139 β = 89.5 c = 74.91 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 2.5 73.25 80.3 0.186 0.201 0.075 0.994 8.5 7.1 21164
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 80.8 1.225 0.577 7
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 2.5 73.25 19893 1115 79.74 0.2435 0.241 0.245 0.2871 0.2903 RANDOM 53.038
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] -2.12 0.06 0.46 -1.48 2.62 4.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.363 r_dihedral_angle_3_deg 13.92 r_dihedral_angle_4_deg 13.451 r_dihedral_angle_1_deg 6.616 r_mcangle_it 6.359 r_mcbond_it 3.849 r_mcbond_other 3.848 r_angle_refined_deg 1.528 r_angle_other_deg 1.11 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.363 r_dihedral_angle_3_deg 13.92 r_dihedral_angle_4_deg 13.451 r_dihedral_angle_1_deg 6.616 r_mcangle_it 6.359 r_mcbond_it 3.849 r_mcbond_other 3.848 r_angle_refined_deg 1.528 r_angle_other_deg 1.11 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4111 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 62
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing MOSFLM data reduction