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Crystal structure of the HIV-1 Rev dimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other An initial model was generated using MAD data sets. This lower resolution model was used for molecular replacement with the final native data set.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 100 mM Tris pH 8.0, 50 mM NaCl, 1.45-1.55 M (NH4)2SO4, 3% PEG1000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.33 47.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.801 α = 90 b = 115.801 β = 90 c = 81.163 γ = 120
Symmetry Space Group P 64 2 2
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 KOHZU: Double Crystal Si(111) 2009-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1159 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.5 50 99.7 0.051 35.2 7.6 11594 11561 49.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.59 99 0.507 3.4 6.1
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MAD; MOLECULAR REPLACEMENT An initial model was generated using MAD data sets. This lower resolution model was used for molecular replacement with the final native data set. 2.5 47.136 0.11 11594 11031 540 95.17 0.2279 0.2262 0.2225 0.2613 0.2572 62.965
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] -2.315 -2.315 4.629
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.175 f_angle_d 0.677 f_chiral_restr 0.044 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1868 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 37
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing PHENIX refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing