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Dpo4 extension ternary complex with oxoG(anti)-G(syn) pair
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GIK PDB entry 3GIK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 100 mM HEPES, 100 mM Calcium acetate, 10% PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.06 59.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.668 α = 90 b = 111.924 β = 90 c = 53.158 γ = 90
Symmetry Space Group P 21 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 6144 x 6144 pixel elements with an effective pixel size less than 60x60 micron and resolution of order 90x90 micron 2005-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97911 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.7 20 93.8 0.093 18.58 6.1 15930
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 72.7 0.493 3 5.1 1198
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 3GIK 2.7 20 15879 797 94.02 0.217 0.214 0.2078 0.277 0.2678 RANDOM 56.274
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] 8.92 -5.51 -3.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.247 r_dihedral_angle_3_deg 18.949 r_dihedral_angle_4_deg 16.441 r_dihedral_angle_1_deg 5.212 r_scangle_it 1.632 r_angle_refined_deg 1.522 r_scbond_it 0.917 r_mcangle_it 0.698 r_mcbond_it 0.431 r_metal_ion_refined 0.347
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.247 r_dihedral_angle_3_deg 18.949 r_dihedral_angle_4_deg 16.441 r_dihedral_angle_1_deg 5.212 r_scangle_it 1.632 r_angle_refined_deg 1.522 r_scbond_it 0.917 r_mcangle_it 0.698 r_mcbond_it 0.431 r_metal_ion_refined 0.347 r_nbtor_refined 0.338 r_nbd_refined 0.265 r_symmetry_vdw_refined 0.259 r_symmetry_hbond_refined 0.255 r_xyhbond_nbd_refined 0.223 r_chiral_restr 0.114 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2740 Nucleic Acid Atoms 630 Solvent Atoms 41 Heterogen Atoms 34
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction AMoRE phasing