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Kinase domain of cSrc in complex with inhibitor RL37 (Type III)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OIQ PDB ENTRY 2OIQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 293 10% PEG 4000, 0.05M sodium acetate, 4% glycerol, 0.1M MES , pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.96 58.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.09 α = 78.94 b = 63.53 β = 89.37 c = 73.99 γ = 90.06
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 2008-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.980890 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 2.5 40 97.2 0.088 13.15 26052 25330 -3 36.777
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 88.7 0.369 3.6
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 2OIQ 2.5 36.59 26052 25328 1014 100 0.224 0.222 0.2191 0.281 0.2745 RANDOM 21.642
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] -0.06 -0.85 0.59 -1.32 0.16 1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.765 r_dihedral_angle_3_deg 19.891 r_dihedral_angle_4_deg 17.79 r_dihedral_angle_1_deg 6.892 r_scangle_it 2.94 r_scbond_it 1.908 r_angle_refined_deg 1.755 r_mcangle_it 1.352 r_mcbond_it 0.792 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.765 r_dihedral_angle_3_deg 19.891 r_dihedral_angle_4_deg 17.79 r_dihedral_angle_1_deg 6.892 r_scangle_it 2.94 r_scbond_it 1.908 r_angle_refined_deg 1.755 r_mcangle_it 1.352 r_mcbond_it 0.792 r_nbtor_refined 0.319 r_symmetry_hbond_refined 0.3 r_symmetry_vdw_refined 0.273 r_nbd_refined 0.239 r_xyhbond_nbd_refined 0.182 r_chiral_restr 0.108 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4191 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 78
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling