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Crystal Structure of UNG2/DNA(TM)
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 7 298 Recombinat 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 DNA duplex (2.5 mM) inclubate at room T for 30 min and then centrifugate at 10000 g for 5 min. Co-crystallization conditions 22-25% PEG 4000, 10mM Hepes pH 6.5, 1mM DTT, 0.5 % v/v dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.57 52.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.499 α = 90 b = 66.318 β = 90 c = 100.316 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 mirrors 2006-01-01 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 36.47 90.4 0.066 43.7 5.8 20504 29.9
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 2.07 55.4 0.247 6.36 3.6
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 (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 36.47 20446 1019 90.74 0.194 0.194 0.192 0.1919 0.238 0.2354 RANDOM 28.728
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] -2.01 0.72 1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.605 r_dihedral_angle_3_deg 12.376 r_dihedral_angle_1_deg 5.172 r_dihedral_angle_4_deg 3.85 r_scangle_it 1.241 r_angle_refined_deg 1.209 r_scbond_it 0.777 r_mcangle_it 0.592 r_mcbond_it 0.353 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.605 r_dihedral_angle_3_deg 12.376 r_dihedral_angle_1_deg 5.172 r_dihedral_angle_4_deg 3.85 r_scangle_it 1.241 r_angle_refined_deg 1.209 r_scbond_it 0.777 r_mcangle_it 0.592 r_mcbond_it 0.353 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.242 r_nbd_refined 0.17 r_symmetry_hbond_refined 0.12 r_xyhbond_nbd_refined 0.108 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1808 Nucleic Acid Atoms 376 Solvent Atoms 398 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing