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Crystal structure of a UNG2/modified DNA complex that represent a stabilized short-lived extrahelical state in ezymatic DNA base flipping
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EMH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 A solution of human UNG2 (22 mg/ml) in 50 mM Tris-OAc buffer pH 7.0, 150 mM NaCl and 1mM DTT was mixed with T/M duplex DNA (2.5 mM)m incubate at room Temperature for 30 min. and then centrifugate at 10000 g for 5 min.Co-crystallizarion condition were 22% PEG 4000, 100 MM HEPES pH 6.5 and 1mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.48 50.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.467 α = 90 b = 65.567 β = 90 c = 98.472 γ = 90
Symmetry Space Group P 21 21 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 IMAGE PLATE RIGAKU RAXIS IV Osmic Mirror 2006-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 2.5 40 97.1 0.162 8.3 4.1 12024 11434 -3.5 50.583
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.59 89.4 0.599 0.59 1.91 3.6 1046
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 1EMH 2.5 29.5 12024 11397 535 94.84 0.257 0.257 0.254 0.2521 0.328 0.3297 RANDOM 39.756
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] -3.73 -2.92 6.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.169 r_dihedral_angle_3_deg 18.191 r_dihedral_angle_4_deg 11.617 r_dihedral_angle_1_deg 6.268 r_angle_refined_deg 1.712 r_scangle_it 1.675 r_scbond_it 1.025 r_mcangle_it 0.773 r_mcbond_it 0.442 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.169 r_dihedral_angle_3_deg 18.191 r_dihedral_angle_4_deg 11.617 r_dihedral_angle_1_deg 6.268 r_angle_refined_deg 1.712 r_scangle_it 1.675 r_scbond_it 1.025 r_mcangle_it 0.773 r_mcbond_it 0.442 r_nbtor_refined 0.308 r_nbd_refined 0.243 r_symmetry_hbond_refined 0.242 r_symmetry_vdw_refined 0.224 r_xyhbond_nbd_refined 0.208 r_chiral_restr 0.137 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1808 Nucleic Acid Atoms 384 Solvent Atoms 107 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction