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Kinase domain of cSrc in complex with inhibitor RL38 (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 3 58.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.01 α = 78.71 b = 63.49 β = 89.71 c = 74.99 γ = 89.91
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 0.978960 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 94.8 0.061 17.03 26267 24911 -3 41.374
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) 2.5 2.75 97 0.233 6.7
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 36.71 26267 24908 872 100 0.246 0.244 0.2648 0.295 0.2951 RANDOM 12.399
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] 0.75 -0.08 0.48 -1.58 0.09 0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.684 r_dihedral_angle_3_deg 19.389 r_dihedral_angle_4_deg 16.137 r_dihedral_angle_1_deg 6.595 r_angle_refined_deg 1.738 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.261 r_symmetry_hbond_refined 0.257 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.684 r_dihedral_angle_3_deg 19.389 r_dihedral_angle_4_deg 16.137 r_dihedral_angle_1_deg 6.595 r_angle_refined_deg 1.738 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.261 r_symmetry_hbond_refined 0.257 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.199 r_chiral_restr 0.112 r_bond_refined_d 0.018 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4189 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 60
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling