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7-Deazapurines and 5-Halogenpyrimidine DNA duplex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EY1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 291 0.2 M Ammonium Sulfate, 0.1 M Sodium acetate trihydrate and 25% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 4.09 69.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.539 α = 90 b = 92.539 β = 90 c = 78.896 γ = 120
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 MARMOSAIC 300 mm CCD 2017-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 2.3 27.6 98.9 0.166 0.044 4.2 13.8 17002
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 90.8 1.471 1.557 0.485 0.595 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.3 27.6 16084 870 98.63 0.21599 0.2139 0.2202 0.25355 0.2613 RANDOM 50.228
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] 1.27 0.63 1.27 -4.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.291 r_dihedral_angle_3_deg 19.294 r_dihedral_angle_4_deg 11.643 r_long_range_B_other 9.494 r_long_range_B_refined 9.492 r_dihedral_angle_1_deg 7.975 r_scangle_other 7.616 r_scbond_it 5.159 r_scbond_other 5.159 r_mcangle_it 4.851
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.291 r_dihedral_angle_3_deg 19.294 r_dihedral_angle_4_deg 11.643 r_long_range_B_other 9.494 r_long_range_B_refined 9.492 r_dihedral_angle_1_deg 7.975 r_scangle_other 7.616 r_scbond_it 5.159 r_scbond_other 5.159 r_mcangle_it 4.851 r_mcangle_other 4.849 r_mcbond_it 3.32 r_mcbond_other 3.3 r_angle_refined_deg 1.567 r_angle_other_deg 0.829 r_chiral_restr 0.402 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 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 1076 Nucleic Acid Atoms 494 Solvent Atoms 79 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction MOLREP phasing