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Cation-dependent self-cleavage activity in the duplex form of the subtype-B HIV-1 RNA Dimerization Initiation Site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OIY PDB ENTRY 2OIY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 310 MgCl2, Na Cacodylate, KCl, spermine, MPD, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 310K
Crystal Properties Matthews coefficient Solvent content 2.02 39.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.689 α = 90 b = 47.541 β = 90 c = 57.735 γ = 90
Symmetry Space Group P 21 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 120 IMAGE PLATE MAC Science DIP-2000 mirror 2002-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.35 20 94.2 0.061 14.1 2.4 9157 8591 62.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.35 2.43 94.6 0.382 2.2 2.4 934
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2OIY 2.4 7.99 2 8838 8059 685 91.2 0.239 0.239 0.2544 0.284 0.2977 RANDOM 42
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] 9.8 -6.56 -3.25
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 9.1 c_improper_angle_d 1.51 c_angle_deg 1.1 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 9.1 c_improper_angle_d 1.51 c_angle_deg 1.1 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 982 Solvent Atoms 46 Heterogen Atoms 5
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing