☰ Navigation Tabs
Crystal structure of a DNA dodecamer containing a tetramethylpyrrolinoxyl (nitroxide) spin label
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D98
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295 Potassium chloride (90 mM),
magnesium chloride (20 mM),
sodium cacodylate (40 mM, pH 6.0),
MPD (45% v/v),
spermine tetrahydrochloride (12 mM)
Crystal Properties Matthews coefficient Solvent content 2.59 52.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.262 α = 90 b = 41.209 β = 90 c = 66.957 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-F 2017-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.915870 Diamond I04
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 2.9 35.09 99 0.045 10.3 3.3 1731
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 2.9 3.1 0.131
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 1d98 2.9 35.09 1621 96 98.4 0.19145 0.18814 0.1909 0.2435 0.253 RANDOM 79.029
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] 3.1 9.82 -12.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 9.784 r_long_range_B_other 9.404 r_long_range_B_refined 9.403 r_scangle_other 8.237 r_scbond_it 5.538 r_scbond_other 5.52 r_angle_other_deg 1.466 r_angle_refined_deg 1.156 r_chiral_restr 0.144 r_gen_planes_refined 0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 9.784 r_long_range_B_other 9.404 r_long_range_B_refined 9.403 r_scangle_other 8.237 r_scbond_it 5.538 r_scbond_other 5.52 r_angle_other_deg 1.466 r_angle_refined_deg 1.156 r_chiral_restr 0.144 r_gen_planes_refined 0.016 r_bond_refined_d 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_mcangle_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 Nucleic Acid Atoms 490 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing