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Crystal structure of d(GGGGTTTTGGGG) with Zn and K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NZ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 30mM NaCaCo(pH6.8), 50mM KCl, 10mM ZnCl2, 2mM Spermine, 5%MPD
Crystal Properties Matthews coefficient Solvent content 2 38.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.457 α = 89.996 b = 47.925 β = 89.916 c = 96.076 γ = 90.059
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 2.49 48.04 91.1 0.891 1.11 4 4651 36
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 2.49 2.554 0.891
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 NONE 2.49 48.038 4239 196 91.142 0.338 0.334 0.3376 0.4258 0.4327 35.832
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] 0.116 0.174 -0.291
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 6.406 r_lrange_other 6.396 r_scangle_it 3.154 r_scangle_other 3.153 r_scbond_other 1.979 r_scbond_it 1.978 r_angle_other_deg 1.602 r_angle_refined_deg 1.175 r_nbd_refined 0.377 r_symmetry_nbd_other 0.264
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 6.406 r_lrange_other 6.396 r_scangle_it 3.154 r_scangle_other 3.153 r_scbond_other 1.979 r_scbond_it 1.978 r_angle_other_deg 1.602 r_angle_refined_deg 1.175 r_nbd_refined 0.377 r_symmetry_nbd_other 0.264 r_nbtor_refined 0.244 r_xyhbond_nbd_refined 0.204 r_metal_ion_refined 0.193 r_nbd_other 0.118 r_symmetry_xyhbond_nbd_other 0.094 r_chiral_restr 0.07 r_symmetry_nbtor_other 0.06 r_symmetry_xyhbond_nbd_refined 0.01 r_gen_planes_refined 0.008 r_symmetry_nbd_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1012 Solvent Atoms 41 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing