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Lyn Tyrosine Kinase Domain-AMP-PNP 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 2.69 54.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.239 α = 90 b = 127.239 β = 90 c = 54.875 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 2.7 38.9 9082
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 2.7 36.74 8665 417 99.87 0.20134 0.19916 0.2584 0.24493 0.2953 RANDOM 32.943
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] 0.38 0.19 0.38 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.984 r_dihedral_angle_3_deg 17.091 r_dihedral_angle_4_deg 11.868 r_dihedral_angle_1_deg 5.424 r_scangle_it 3.4 r_scbond_it 2.332 r_mcangle_it 1.51 r_angle_refined_deg 1.153 r_mcbond_it 0.815 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.984 r_dihedral_angle_3_deg 17.091 r_dihedral_angle_4_deg 11.868 r_dihedral_angle_1_deg 5.424 r_scangle_it 3.4 r_scbond_it 2.332 r_mcangle_it 1.51 r_angle_refined_deg 1.153 r_mcbond_it 0.815 r_nbtor_refined 0.307 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.14 r_xyhbond_nbd_refined 0.112 r_symmetry_hbond_refined 0.097 r_chiral_restr 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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 15 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement