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Low Temperature joint X-ray/neutron structure of DNA oligonucleotide d(GTGGCCAC)2 with 2'-SeCH3 modification on Cyt5
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FP6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 303 0.1 M magnesium acetate, 30% MPD, 0.1 M MES
Crystal Properties Matthews coefficient Solvent content 2.06 40.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.884 α = 90 b = 41.884 β = 90 c = 24.307 γ = 90
Symmetry Space Group P 43 21 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 IMAGE PLATE RIGAKU RAXIS IV++ osmic varimax 2017-12-12 M SINGLE WAVELENGTH 2 1 neutron 100 IMAGE PLATE LADI III collimators 2017-11-20 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54 2 NUCLEAR REACTOR ILL BEAMLINE LADI III 2.8-4.0 ILL LADI III
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (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 1.65 40 100 0.056 16.6 10.4 2866 2 1.9 21.3 84.6 0.179 9.1 7 1629
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.71 0.149 10.2 2 1.9 2 0.226 3.4
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 1.65 40 2.5 2843 2800 136 98.2 0.23 0.2317 0.246 0.2397 random 24.54 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 1.9 21.3 2.5 1909 1572 65 82.3 0.234 0.26 random 24.54
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]
RMS Deviations Key Refinement Restraint Deviation x_torsion_impr_deg 0.95 x_torsion_impr_deg 0.95 x_angle_deg 0.9 x_angle_deg 0.9 x_torsion_deg 0.7 x_torsion_deg 0.7 x_bond_d 0.006 x_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 163 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 2
Software Software Software Name Purpose nCNS refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing LAUEGEN data reduction LSCALE data scaling CNS phasing