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oxoG-modified Insertion Ternary Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JX4 PDB ENTRY 1JX4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 PEG 4000, HEPES-sodium, calcium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 3.3 62.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.955 α = 90 b = 101.109 β = 97.14 c = 84.124 γ = 90
Symmetry Space Group P 1 21 1
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 MARRESEARCH 2003-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 0.9000 APS 14-ID-B
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 1.9 50 99.2 0.039 4.5 98435
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 1.9 1.94 98.7 0.671 3.4 6523
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 PDB ENTRY 1JX4 1.95 20 86555 86555 4508 99.26 0.226 0.226 0.22459 0.2318 0.25255 0.2324 RANDOM 15.648
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] -0.08 -0.23 1.38 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.04 r_scangle_it 1.741 r_angle_refined_deg 1.316 r_scbond_it 1.061 r_angle_other_deg 0.826 r_mcangle_it 0.762 r_mcbond_it 0.404 r_symmetry_vdw_other 0.316 r_symmetry_vdw_refined 0.235 r_nbd_other 0.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.04 r_scangle_it 1.741 r_angle_refined_deg 1.316 r_scbond_it 1.061 r_angle_other_deg 0.826 r_mcangle_it 0.762 r_mcbond_it 0.404 r_symmetry_vdw_other 0.316 r_symmetry_vdw_refined 0.235 r_nbd_other 0.211 r_nbd_refined 0.18 r_xyhbond_nbd_refined 0.138 r_symmetry_hbond_refined 0.111 r_metal_ion_refined 0.103 r_chiral_restr 0.101 r_nbtor_other 0.078 r_bond_refined_d 0.007 r_bond_other_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5478 Nucleic Acid Atoms 1259 Solvent Atoms 501 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing