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Crystal structure of d(GCCCACCACGGC)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other X3DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 20%MPD, 120mMMgCl2, 60mM NaCaCo, 2mM Spermine
Crystal Properties Matthews coefficient Solvent content 2.52 51.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.49 α = 90 b = 64.49 β = 90 c = 46.19 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 270 PIXEL DECTRIS PILATUS 2M 2022-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 2.00 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.95 35.59 96.95 0.992 2 9.2 2783
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.97 3.02 0.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE X3DNA 2.955 35.59 1461 62 96.948 0.129 0.125 0.1292 0.2298 0.2391 88.593
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] -0.113 -0.057 -0.113 0.368
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 8.351 r_lrange_other 8.351 r_scangle_it 6.768 r_scangle_other 6.756 r_scbond_it 4.636 r_scbond_other 4.607 r_angle_other_deg 1.751 r_angle_refined_deg 1.196 r_symmetry_nbd_refined 0.343 r_nbd_other 0.301
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 8.351 r_lrange_other 8.351 r_scangle_it 6.768 r_scangle_other 6.756 r_scbond_it 4.636 r_scbond_other 4.607 r_angle_other_deg 1.751 r_angle_refined_deg 1.196 r_symmetry_nbd_refined 0.343 r_nbd_other 0.301 r_symmetry_nbd_other 0.265 r_nbtor_refined 0.256 r_nbd_refined 0.13 r_xyhbond_nbd_refined 0.122 r_symmetry_xyhbond_nbd_other 0.116 r_symmetry_nbtor_other 0.07 r_chiral_restr 0.069 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 492 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing