☰ Navigation Tabs
Structural descriptions of ligand interactions to DNA and RNA quadruplexes folded from the non-coding region of Pseudorabies virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JJH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 283 Potassium cacodylate, Potassium chloride, Sodium cacodylate, MPD
Crystal Properties Matthews coefficient Solvent content 2.05 39.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.177 α = 90 b = 43.974 β = 108.39 c = 30.781 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2019-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96864 Diamond I24
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 1.21 27.703 94.1 0.066 0.072 0.028 0.998 11.8 5.7 21248
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.21 1.23 56.5 0.599 0.718 0.387 0.853 3.1
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-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 FREE R-VALUE 6JJH 1.21 27.69 21227 1025 93.879 0.2 0.1999 0.199 0.2015 0.217 0.2216 Random Selection 17.82
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] -0.412 -0.107 1.5 -0.833
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.1 r_lrange_other 3.947 r_scangle_it 2.943 r_scangle_other 2.828 r_angle_refined_deg 2.001 r_scbond_it 1.917 r_scbond_other 1.832 r_angle_other_deg 1.82 r_nbtor_refined 0.274 r_nbd_refined 0.237
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.1 r_lrange_other 3.947 r_scangle_it 2.943 r_scangle_other 2.828 r_angle_refined_deg 2.001 r_scbond_it 1.917 r_scbond_other 1.832 r_angle_other_deg 1.82 r_nbtor_refined 0.274 r_nbd_refined 0.237 r_symmetry_nbd_other 0.228 r_nbd_other 0.203 r_symmetry_nbd_refined 0.129 r_chiral_restr 0.12 r_xyhbond_nbd_refined 0.12 r_symmetry_xyhbond_nbd_refined 0.068 r_symmetry_nbtor_other 0.063 r_metal_ion_refined 0.063 r_gen_planes_refined 0.032 r_bond_refined_d 0.025 r_gen_planes_other 0.005 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 606 Solvent Atoms 97 Heterogen Atoms 119
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction