☰ Navigation Tabs
Lyn Tyrosine Kinase Domain, apo form
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 2.64 53.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.31 α = 90 b = 127.31 β = 90 c = 53.836 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 2.5 63.3 11259
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 2.5 38.52 10743 516 99.98 0.20638 0.2048 0.2744 0.2378 0.2809 RANDOM 29.88
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] 0.26 0.13 0.26 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.41 r_dihedral_angle_3_deg 17.137 r_dihedral_angle_4_deg 14.197 r_dihedral_angle_1_deg 5.296 r_scangle_it 3.46 r_scbond_it 2.395 r_mcangle_it 1.561 r_angle_refined_deg 1.035 r_mcbond_it 0.853 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.41 r_dihedral_angle_3_deg 17.137 r_dihedral_angle_4_deg 14.197 r_dihedral_angle_1_deg 5.296 r_scangle_it 3.46 r_scbond_it 2.395 r_mcangle_it 1.561 r_angle_refined_deg 1.035 r_mcbond_it 0.853 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.201 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.141 r_xyhbond_nbd_refined 0.117 r_chiral_restr 0.07 r_bond_refined_d 0.007 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 2044 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement