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chicken c-Src kinase domain in complex with ATPgS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2SRC 2SRC with deletion of residues 300-315 and 400-425
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 10% PEG 4000, 50 mM Ammonium acetate, 100 mM Bis-Tris pH 5.5, 5% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 50.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.507 α = 90 b = 119.15 β = 90.36 c = 63.676 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2004-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.1 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.3 50 96.6 0.062 0.062 18 3.6 27164 27164
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 81.4 0.205 0.205 4.49 3
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 2SRC with deletion of residues 300-315 and 400-425 2.3 34.61 25766 25766 1370 96.39 0.19385 0.19123 0.1893 0.24131 0.2363 RANDOM 53.856
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] 0.3 -0.1 -0.22 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.023 r_dihedral_angle_3_deg 17.894 r_dihedral_angle_4_deg 15.686 r_dihedral_angle_1_deg 5.746 r_scangle_it 2.592 r_scbond_it 1.648 r_angle_refined_deg 1.263 r_mcangle_it 0.917 r_mcbond_it 0.481 r_symmetry_hbond_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.023 r_dihedral_angle_3_deg 17.894 r_dihedral_angle_4_deg 15.686 r_dihedral_angle_1_deg 5.746 r_scangle_it 2.592 r_scbond_it 1.648 r_angle_refined_deg 1.263 r_mcangle_it 0.917 r_mcbond_it 0.481 r_symmetry_hbond_refined 0.311 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.202 r_nbd_refined 0.183 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4299 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling PHASER phasing