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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 2.15 42.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.695 α = 90 b = 42.695 β = 90 c = 24.41 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 293 IMAGE PLATE RIGAKU RAXIS IV++ osmic varimax 2015-01-22 M SINGLE WAVELENGTH 2 1 neutron 293 IMAGE PLATE LADI III collimators 2015-08-15 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 1.56 40 96.8 0.033 45.8 6.7 3414 2 2 20 74.2 0.176 7.7 5.6 1257
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 1.56 1.62 0.417 3.3 2 2 2.11 0.289 2.8
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 1.56 40 2.5 3484 2960 198 84.6 0.242 0.2369 0.276 0.262 random 27.66 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2 20 2.5 1717 1204 64 70 0.25 0.312 random 27.66
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 1.03 x_torsion_impr_deg 1.03 x_angle_deg 1 x_angle_deg 1 x_torsion_deg 0.5 x_torsion_deg 0.5 x_bond_d 0.007 x_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 163 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 1
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