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Kinase domain of cSrc in complex with RL130
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F3V PDB ENTRY 3F3V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 10% PEG 20000, 15% glycerol, 100mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.97 58.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.02 α = 79.6 b = 63.42 β = 87.89 c = 74.2 γ = 89.98
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD MARRESEARCH Dynamically bendable mirror 2010-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.003900 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.1 45 91.8 0.062 9.61 1.79 13657 12539 -3 43.513
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.2 93.7 0.205 0.29 4 1.84 1245
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 PDB ENTRY 3F3V 3.1 41.99 13657 12538 815 100 0.2162 0.2115 0.209 0.2832 0.2763 RANDOM 53.022
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] -1.31 -0.72 0.77 -3.62 0.96 4.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.99 r_dihedral_angle_4_deg 20.716 r_dihedral_angle_3_deg 20.492 r_dihedral_angle_1_deg 6.448 r_scangle_it 1.864 r_angle_refined_deg 1.363 r_scbond_it 1.139 r_mcangle_it 0.98 r_mcbond_it 0.546 r_symmetry_hbond_refined 0.347
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.99 r_dihedral_angle_4_deg 20.716 r_dihedral_angle_3_deg 20.492 r_dihedral_angle_1_deg 6.448 r_scangle_it 1.864 r_angle_refined_deg 1.363 r_scbond_it 1.139 r_mcangle_it 0.98 r_mcbond_it 0.546 r_symmetry_hbond_refined 0.347 r_nbtor_refined 0.319 r_symmetry_vdw_refined 0.262 r_nbd_refined 0.24 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4194 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 74
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction SLS-Software data collection XDS data reduction