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Dpo4 extension ternary complex with the oxoG(anti)-C(anti) pair
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GII PDB entry 3GII
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 3.04 59.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.855 α = 90 b = 112.399 β = 90 c = 52.834 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 24-ID-C 0.97949 APS 24-ID-C
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 2.87 20 94.9 0.089 15.9 4.7 13271 12594
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 2.87 2.96 84.1 0.656 1.8
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 3GII 2.9 20 12594 651 95.06 0.234 0.232 0.2344 0.277 0.2772 RANDOM 42.478
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] 10.81 -6.58 -4.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.517 r_dihedral_angle_3_deg 19.211 r_dihedral_angle_4_deg 17.182 r_dihedral_angle_1_deg 5.567 r_scangle_it 1.628 r_angle_refined_deg 1.609 r_scbond_it 0.969 r_mcangle_it 0.676 r_mcbond_it 0.435 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.517 r_dihedral_angle_3_deg 19.211 r_dihedral_angle_4_deg 17.182 r_dihedral_angle_1_deg 5.567 r_scangle_it 1.628 r_angle_refined_deg 1.609 r_scbond_it 0.969 r_mcangle_it 0.676 r_mcbond_it 0.435 r_chiral_restr 0.122 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2740 Nucleic Acid Atoms 627 Solvent Atoms 17 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing