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Crystal structure of d(CCGGGGTACCCCGG) with XRB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WV7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 8%MPD, 1mM BaCl2, 5mM Spermine
Crystal Properties Matthews coefficient Solvent content 2.26 45.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.76 α = 90 b = 41.76 β = 90 c = 88.96 γ = 90
Symmetry Space Group P 41 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 270 PIXEL DECTRIS PILATUS 2M 2022-08-03 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) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.837 37.8 98.83 0.114 0.12 0.038 0.996 50.8 10.4 7419
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 1.837 1.885 90.94 0.716
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 FREE R-VALUE 5WV7 1.837 37.8 7295 361 98.835 0.144 0.1415 0.1385 0.1927 0.1813 43.764
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] 0.012 0.012 -0.024
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.787 r_lrange_other 5.784 r_scangle_it 2.47 r_scangle_other 2.469 r_scbond_other 1.856 r_scbond_it 1.855 r_angle_refined_deg 1.741 r_angle_other_deg 1.383 r_symmetry_xyhbond_nbd_refined 0.476 r_nbtor_refined 0.269
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.787 r_lrange_other 5.784 r_scangle_it 2.47 r_scangle_other 2.469 r_scbond_other 1.856 r_scbond_it 1.855 r_angle_refined_deg 1.741 r_angle_other_deg 1.383 r_symmetry_xyhbond_nbd_refined 0.476 r_nbtor_refined 0.269 r_nbd_other 0.251 r_symmetry_nbd_other 0.211 r_symmetry_nbd_refined 0.153 r_chiral_restr 0.152 r_nbd_refined 0.084 r_symmetry_nbtor_other 0.058 r_xyhbond_nbd_refined 0.035 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 568 Solvent Atoms Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing