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Dpo4 extension ternary complex with disordered A opposite an oxoG in anti conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ASD PDB entry 2ASD
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 2.89 57.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.761 α = 90 b = 111.646 β = 90 c = 52.708 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 0.97942 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 2.6 20 94.2 0.096 16.2 6.2 17030 16924
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 2.6 2.67 71.7 0.528 2.6 975
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 2ASD 2.6 20 16924 856 94.18 0.205 0.202 0.2042 0.265 0.263 RANDOM 49.029
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] 5.08 -1.85 -3.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.715 r_dihedral_angle_4_deg 20.422 r_dihedral_angle_3_deg 17.969 r_dihedral_angle_1_deg 5.248 r_scangle_it 1.837 r_angle_refined_deg 1.651 r_scbond_it 1.152 r_angle_other_deg 0.923 r_mcangle_it 0.843 r_mcbond_it 0.472
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.715 r_dihedral_angle_4_deg 20.422 r_dihedral_angle_3_deg 17.969 r_dihedral_angle_1_deg 5.248 r_scangle_it 1.837 r_angle_refined_deg 1.651 r_scbond_it 1.152 r_angle_other_deg 0.923 r_mcangle_it 0.843 r_mcbond_it 0.472 r_symmetry_vdw_refined 0.267 r_metal_ion_refined 0.261 r_symmetry_vdw_other 0.225 r_nbd_refined 0.213 r_nbd_other 0.195 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.19 r_symmetry_hbond_refined 0.142 r_chiral_restr 0.11 r_nbtor_other 0.082 r_mcbond_other 0.063 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_xyhbond_nbd_other 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2740 Nucleic Acid Atoms 628 Solvent Atoms 66 Heterogen Atoms 35
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