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crystal structure of a DNA duplex containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EHV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 25mM Sodium cacodylate (pH7.0), 6mM Spermine, tetrahydrochloride, 50mM NaCl, 5% MPD , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.74 55.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.477 α = 90 b = 26.477 β = 90 c = 98.958 γ = 120
Symmetry Space Group P 32 1 2
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 270 mirrors 2006-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.00 Photon Factory AR-NW12A
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 1.92 50 99.4 0.064 91.6 20.7 3233 3233
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) 1.92 1.99 100 0.291 15.9 21.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1ehv 1.92 22.34 2 3205 3165 139 99.3 0.227 0.227 0.225 0.2285 0.264 0.2372 RANDOM 25.343
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] -0.06 -0.03 -0.06 0.09
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.407 r_angle_refined_deg 2.209 r_scbond_it 1.798 r_symmetry_metal_ion_refined 0.457 r_symmetry_vdw_refined 0.447 r_metal_ion_refined 0.443 r_nbtor_refined 0.312 r_xyhbond_nbd_refined 0.186 r_nbd_refined 0.154 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.407 r_angle_refined_deg 2.209 r_scbond_it 1.798 r_symmetry_metal_ion_refined 0.457 r_symmetry_vdw_refined 0.447 r_metal_ion_refined 0.443 r_nbtor_refined 0.312 r_xyhbond_nbd_refined 0.186 r_nbd_refined 0.154 r_chiral_restr 0.086 r_symmetry_hbond_refined 0.062 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 246 Solvent Atoms 42 Heterogen Atoms 1
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling