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c-Src 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, 10% PEG 3350, 3% glycerol, 10 mM NaOAC, 10 mM DTT
Crystal Properties Matthews coefficient Solvent content 3.22 61.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.675 α = 102.08 b = 63.922 β = 90.36 c = 74.994 γ = 90.14
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 2016-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 73.33 81.8 0.161 0.988 3.5 2.6 21425
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 79.3 1.673 0.401 2.2
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 73.33 18903 1045 76.15 0.2673 0.2642 0.2667 0.3232 0.3261 RANDOM 80.726
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] -7.98 0.45 1.38 -0.8 -4.84 9.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.699 r_dihedral_angle_3_deg 15.226 r_dihedral_angle_4_deg 10.093 r_mcangle_it 8.39 r_dihedral_angle_1_deg 6.84 r_mcbond_it 5.127 r_mcbond_other 5.125 r_angle_refined_deg 1.452 r_angle_other_deg 0.956 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.699 r_dihedral_angle_3_deg 15.226 r_dihedral_angle_4_deg 10.093 r_mcangle_it 8.39 r_dihedral_angle_1_deg 6.84 r_mcbond_it 5.127 r_mcbond_other 5.125 r_angle_refined_deg 1.452 r_angle_other_deg 0.956 r_chiral_restr 0.08 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 4199 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 62
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing