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Structure of the 10S (+)-trans-BP-dG modified Rev1 ternary complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AQ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.25 M sodium citrate pH 6.0 buffer
15-20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.33 47.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.002 α = 90 b = 64.879 β = 90 c = 130.652 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 PIXEL DECTRIS PILATUS 6M 2013-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.85 45 99.7 26.3 7.2 47446
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 2AQ4 1.85 65.33 44991 2389 99.5 0.17195 0.17012 0.1794 0.20649 0.2126 RANDOM 25.19
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] -1.05 1.01 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.254 r_dihedral_angle_4_deg 16.777 r_dihedral_angle_3_deg 12.502 r_dihedral_angle_1_deg 5.691 r_long_range_B_refined 5.011 r_long_range_B_other 4.857 r_scangle_other 3.101 r_mcangle_it 2.276 r_mcangle_other 2.276 r_scbond_it 1.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.254 r_dihedral_angle_4_deg 16.777 r_dihedral_angle_3_deg 12.502 r_dihedral_angle_1_deg 5.691 r_long_range_B_refined 5.011 r_long_range_B_other 4.857 r_scangle_other 3.101 r_mcangle_it 2.276 r_mcangle_other 2.276 r_scbond_it 1.959 r_scbond_other 1.956 r_mcbond_it 1.421 r_mcbond_other 1.421 r_angle_refined_deg 1.383 r_angle_other_deg 1 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3443 Nucleic Acid Atoms 571 Solvent Atoms 335 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing