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Crystal structure bacteriohage T5 D15 flap endonuclease (D155K) pseudo-enzyme-product complex with DNA and metal ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HML
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 290 Oligonucleotides was adjusted to 1.1 mM for the duplex molecule by dissolving each one in 10 mM MES pH 6.5 and 50 mM KCl. T5FenD155K with oligonucleotide 3ov6 prepared above, grew in 0.2 M CaCl2, 0.1 M sodium acetate buffer pH 5, 20% w/v PEG 6000.
Crystal Properties Matthews coefficient Solvent content 2.96 58.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.51 α = 90 b = 67.51 β = 90 c = 187.81 γ = 90
Symmetry Space Group P 43 21 2
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 2011-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9796 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.861 67.51 99.8 0.08 0.083 0.016 30.8 27.9 37488 37488
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.91 99.7 1.043 1.043 0.198 0.6 28.8 2720
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 5HML 1.86 54.81 35532 1871 99.8 0.1595 0.158 0.1692 0.1883 0.1963 RANDOM 38.372
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] 1.15 1.15 -2.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.008 r_dihedral_angle_3_deg 13.563 r_dihedral_angle_4_deg 11.674 r_mcangle_it 5.717 r_mcbond_it 5.341 r_mcbond_other 5.019 r_dihedral_angle_1_deg 4.937 r_angle_refined_deg 1.371 r_angle_other_deg 1.03 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.008 r_dihedral_angle_3_deg 13.563 r_dihedral_angle_4_deg 11.674 r_mcangle_it 5.717 r_mcbond_it 5.341 r_mcbond_other 5.019 r_dihedral_angle_1_deg 4.937 r_angle_refined_deg 1.371 r_angle_other_deg 1.03 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2194 Nucleic Acid Atoms 345 Solvent Atoms 218 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction xia2 data reduction PHASER phasing