☰ Navigation Tabs
Crystal structure of the FHA domain of mouse polynucleotide kinase in complex with an XRCC4-derived phosphopeptide.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YJ5 The FHA domain from the full-length mouse PNK structure, 1YJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.1M Na citrate (pH 5.5), 25% PEG 4000, 0.2M Li2SO4, 5mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.06 59.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.155 α = 90 b = 122.999 β = 90 c = 136.71 γ = 90
Symmetry Space Group C 2 2 21
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 4 2004-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1159 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 50 89.4 0.051 8.8 2.7 21246 18994 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 70.2 0.194 3.4
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 (All) 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 The FHA domain from the full-length mouse PNK structure, 1YJ5 2.2 50 21246 18994 1022 89.49 0.21253 0.21253 0.21088 0.222 0.24278 0.2454 RANDOM 25.637
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] 0.21 -0.74 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.548 r_dihedral_angle_3_deg 10.997 r_dihedral_angle_4_deg 10.402 r_dihedral_angle_1_deg 5.026 r_angle_refined_deg 0.862 r_angle_other_deg 0.669 r_scangle_it 0.43 r_scbond_it 0.282 r_mcangle_it 0.208 r_mcbond_it 0.192
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.548 r_dihedral_angle_3_deg 10.997 r_dihedral_angle_4_deg 10.402 r_dihedral_angle_1_deg 5.026 r_angle_refined_deg 0.862 r_angle_other_deg 0.669 r_scangle_it 0.43 r_scbond_it 0.282 r_mcangle_it 0.208 r_mcbond_it 0.192 r_symmetry_vdw_refined 0.167 r_nbd_refined 0.163 r_nbtor_refined 0.157 r_nbd_other 0.149 r_symmetry_vdw_other 0.101 r_xyhbond_nbd_refined 0.082 r_symmetry_hbond_refined 0.077 r_nbtor_other 0.07 r_chiral_restr 0.055 r_mcbond_other 0.022 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2531 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing