☰ Navigation Tabs
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, SITTING DROP 7 293 20mM Sodium cacodylate (pH7.0), 6mM Spermine tetrahydrochloride, 6mM NaCl, 40mM KCl, 5% MPD
, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.69 54.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.221 α = 90 b = 26.221 β = 90 c = 99.016 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 315 mirrors 2006-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00 Photon Factory BL-5A
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 2.2 50 98.9 0.052 70.4 9.5 2137 2137
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) 2.2 2.28 100 0.307 11.3 8.8
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 2.2 18.7 2 2110 2071 92 99.3 0.261 0.255 0.252 0.2332 0.314 0.2421 RANDOM 40.346
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] 1.68 0.84 1.68 -2.52
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.879 r_angle_refined_deg 4.351 r_scbond_it 3.584 r_symmetry_metal_ion_refined 0.905 r_symmetry_vdw_refined 0.515 r_symmetry_hbond_refined 0.431 r_metal_ion_refined 0.395 r_nbtor_refined 0.363 r_nbd_refined 0.3 r_xyhbond_nbd_refined 0.196
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.879 r_angle_refined_deg 4.351 r_scbond_it 3.584 r_symmetry_metal_ion_refined 0.905 r_symmetry_vdw_refined 0.515 r_symmetry_hbond_refined 0.431 r_metal_ion_refined 0.395 r_nbtor_refined 0.363 r_nbd_refined 0.3 r_xyhbond_nbd_refined 0.196 r_chiral_restr 0.144 r_bond_refined_d 0.029 r_gen_planes_refined 0.016 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 35 Heterogen Atoms 1
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling