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c-Src V281C kinase domain in complex with Rao-IV-156
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5SWH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 298 100 mM MES pH 6.3, 40 mM NaOAc, 8% PEG3350, 10% glycerol, 10 mM DTT
Crystal Properties Matthews coefficient Solvent content 3.27 62.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.79 α = 76.73 b = 63.59 β = 89.93 c = 76.07 γ = 89.79
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 2016-07-17 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 3 74.04 79.8 0.168 0.202 0.111 0.893 6 3.4 12160
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 3 3.18 83.6 0.31 0.365 0.192 0.876 3.5 2073
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 5SWH 2.99 74.04 11499 661 78.94 0.3069 0.3036 0.2772 0.3659 0.321 RANDOM 77.268
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] -37.91 -14.19 0.46 53.44 12.16 -15.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.566 r_dihedral_angle_4_deg 18.87 r_dihedral_angle_3_deg 17.895 r_dihedral_angle_1_deg 9.734 r_angle_refined_deg 2.027 r_angle_other_deg 1.155 r_chiral_restr 0.106 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.566 r_dihedral_angle_4_deg 18.87 r_dihedral_angle_3_deg 17.895 r_dihedral_angle_1_deg 9.734 r_angle_refined_deg 2.027 r_angle_other_deg 1.155 r_chiral_restr 0.106 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4200 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing