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Lyn Tyrosine Kinase Domain-PP2 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QPD PDB ENTRY 1QPD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 23% polyethylene glycol 3350, 0.1M NaCl, 0.1M Na-Hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.7 54.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.468 α = 90 b = 128.468 β = 90 c = 54.169 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.54180
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.76 48.7 8337
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 PDB ENTRY 1QPD 2.76 33.22 7954 381 97.12 0.19671 0.19499 0.2454 0.23118 0.2568 RANDOM 12.426
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] 0.03 0.01 0.03 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.913 r_dihedral_angle_4_deg 19.876 r_dihedral_angle_3_deg 16.881 r_dihedral_angle_1_deg 6.265 r_scangle_it 3.052 r_scbond_it 1.939 r_mcangle_it 1.55 r_angle_refined_deg 1.235 r_mcbond_it 0.838 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.913 r_dihedral_angle_4_deg 19.876 r_dihedral_angle_3_deg 16.881 r_dihedral_angle_1_deg 6.265 r_scangle_it 3.052 r_scbond_it 1.939 r_mcangle_it 1.55 r_angle_refined_deg 1.235 r_mcbond_it 0.838 r_nbtor_refined 0.312 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.165 r_symmetry_hbond_refined 0.131 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 2031 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement