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The atomic structure of 5-Hydroxymethyl 2'-deoxycitidine base paired with 2'-deoxyguanosine in Dickerson Drew Dodecamer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 436D PDB ENTRY 436D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 10% MPD,40mM cacodylate, 80mM NaCl,12 mM spermine tetrachloride, 20mM MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.3 46.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.606 α = 90 b = 41.344 β = 90 c = 64.319 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 CCD ADSC QUANTUM 315r mirrors 2012-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
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 1.02 14.9 98 0.043 44.67 8.8 36693 35974 2 2
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 1.02 1.03 99.9 0.78 6.5
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 (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 436D 1.02 14.88 33816 32113 1700 95.04 0.16064 0.15947 0.1694 0.18189 0.1857 RANDOM 22.675
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] 0.24 -1.49 1.26
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 10.669 r_sphericity_free 8.84 r_rigid_bond_restr 4.594 r_angle_other_deg 2.562 r_angle_refined_deg 2.488 r_chiral_restr 0.406 r_gen_planes_refined 0.041 r_bond_refined_d 0.02 r_gen_planes_other 0.008 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 10.669 r_sphericity_free 8.84 r_rigid_bond_restr 4.594 r_angle_other_deg 2.562 r_angle_refined_deg 2.488 r_chiral_restr 0.406 r_gen_planes_refined 0.041 r_bond_refined_d 0.02 r_gen_planes_other 0.008 r_bond_other_d 0.006 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 490 Solvent Atoms 187 Heterogen Atoms 26
Software Software Software Name Purpose SBC-Collect data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling