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STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE (RT) TERNARY COMPLEX WITH A DOUBLE STRANDED DNA AND AN INCOMING D4TTP AT PH 9.5 WITH CROSS-LINKING TO SECOND BASE TEMPLATE OVERHANG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AMO PDBID 6AMO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 277 PEG 8000, NaCl, CHES (N-Cyclohexyl-2-aminoethanesulfonic acid), TRIS, MgCl2, d4T triphosphate
Crystal Properties Matthews coefficient Solvent content 3.2 61.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.264 α = 90 b = 133.333 β = 97.63 c = 140.203 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 270 White beam collimating mirror, horizontally focusing monochromator using single bent triangular Si(111) crystal, vertically focusing Rh-coated Si mirror 2010-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.9186 CHESS F1
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 99.3 0.101 17 6.6 112162 54.62
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) 1 2.5 2.59 99.7 0.785 1.8 5.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDBID 6AMO 2.502 34.372 1.36 112126 2003 98.91 0.1916 0.191 0.1915 0.2291 0.2282 92.9455
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 12.939 f_angle_d 0.443 f_chiral_restr 0.04 f_bond_d 0.006 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15778 Nucleic Acid Atoms 1716 Solvent Atoms 661 Heterogen Atoms 132
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction Coot model building