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Crystal structure of d(CGTGAATTCACG) with HT1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JU4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 10%MPD, 60mM MgCl2, 30 mM NaCaCo (pH6.8), 1mM Spermine
Crystal Properties Matthews coefficient Solvent content 2.21 44.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.593 α = 90 b = 40.406 β = 90 c = 65.033 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 294 PIXEL DECTRIS PILATUS 2M 2022-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 2 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 1.902 34.321 99.8 0.964 4.36 7 5462 39.4
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 1.902 1.951 0.964
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.902 34.321 5451 251 99.817 0.221 0.2193 0.2265 0.2465 0.2595 37.124
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] -0.002 -0.001 0.002
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 8.776 r_lrange_it 8.586 r_scangle_it 4.823 r_scangle_other 4.82 r_scbond_it 3.49 r_scbond_other 3.488 r_angle_refined_deg 1.809 r_angle_other_deg 1.691 r_metal_ion_refined 0.285 r_symmetry_nbd_refined 0.276
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 8.776 r_lrange_it 8.586 r_scangle_it 4.823 r_scangle_other 4.82 r_scbond_it 3.49 r_scbond_other 3.488 r_angle_refined_deg 1.809 r_angle_other_deg 1.691 r_metal_ion_refined 0.285 r_symmetry_nbd_refined 0.276 r_nbtor_refined 0.247 r_nbd_other 0.217 r_symmetry_nbd_other 0.216 r_xyhbond_nbd_refined 0.159 r_nbd_refined 0.147 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.087 r_symmetry_xyhbond_nbd_refined 0.073 r_gen_planes_refined 0.018 r_bond_other_d 0.016 r_bond_refined_d 0.009 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 486 Solvent Atoms 18 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing