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HIV-1 Rev Response Element (RRE) Stem-Loop II (SLII)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LYG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 100 mM SPG (mixture of succinic acid, sodium dihydrogen phosphate, and glycine in a 2:7:7 molar ratio), 20-24% polyethylene glycol-6000, and 200 mM sodium fluoride
Crystal Properties Matthews coefficient Solvent content 2.55 51.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.782 α = 90 b = 81.314 β = 99.14 c = 81.372 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 CCD ADSC QUANTUM 315r 2023-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.85 57.2 88.5 0.1 0.05 0.999 8.9 4 12674 66.82
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 3.2 0.72 0.487 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.85 57.15 1.34 12666 605 61.41 0.2326 0.2314 0.2316 0.2578 0.258 114.73
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.4104 f_angle_d 0.7561 f_chiral_restr 0.0378 f_plane_restr 0.0046 f_bond_d 0.0026
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 5742 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose autoPROC data processing XDS data scaling PHENIX phasing PHENIX model building PHENIX refinement XDS data reduction