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Structure of the 10S (-)-cis-BP-dG modified Rev1 ternary complex (the BP residue is disordered)
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 2.34 47.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.307 α = 90 b = 65.476 β = 90 c = 131.657 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 1.10 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 2.25 65.83 100 18.6 7.4 26824
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 2.25 65.83 25424 1345 99.82 0.17223 0.1699 0.1787 0.2171 0.2199 RANDOM 38.837
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] -1.3 1.91 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.036 r_dihedral_angle_4_deg 16.709 r_dihedral_angle_3_deg 15.223 r_long_range_B_refined 7.421 r_long_range_B_other 7.404 r_dihedral_angle_1_deg 5.861 r_scangle_other 5.243 r_mcangle_other 3.534 r_mcangle_it 3.533 r_scbond_it 3.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.036 r_dihedral_angle_4_deg 16.709 r_dihedral_angle_3_deg 15.223 r_long_range_B_refined 7.421 r_long_range_B_other 7.404 r_dihedral_angle_1_deg 5.861 r_scangle_other 5.243 r_mcangle_other 3.534 r_mcangle_it 3.533 r_scbond_it 3.295 r_scbond_other 3.28 r_mcbond_it 2.26 r_mcbond_other 2.257 r_angle_refined_deg 1.474 r_angle_other_deg 1.011 r_chiral_restr 0.086 r_bond_refined_d 0.011 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 3436 Nucleic Acid Atoms 552 Solvent Atoms 161 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing