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HIV-1 Reverse Transcriptase with the Inhibitor beta-Thujaplicinol Bound at the RNase H Active Site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DLO PDB ENTRY 1DLO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 277 50 mM Bicine pH 8.2, 45 mM Ammonium Sulfate, 15 mM Manganese Sulfate, 10 mM Spermine, 5 mM Taurine, 2% PEG 400, 10% PEG 8000
Combined with equal volume of: 10 mM Tris pH 8.0, 75 mM NaCl, 3.5% DMSO, 0.86 mM b-Thujaplicinol, 0.17 mM Reverse Transcriptase, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.69 54.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.057 α = 90 b = 71.3 β = 105.13 c = 108.541 γ = 90
Symmetry Space Group C 1 2 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 315 2007-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.08 NSLS X25
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 2.8 35 94.3 0.061 15.3 2.7 28769 28769 -1.1 71.5
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) 2.8 2.9 77.2 0.489 2.1 2599
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 THROUGHOUT PDB ENTRY 1DLO 2.8 33.75 30078 27627 784 91.9 0.241 0.238 0.238 0.2361 0.255 0.2555 RANDOM 89.018
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] -13.53 6.1 -6.74 20.26
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.1 c_scangle_it 8.36 c_mcangle_it 5.87 c_scbond_it 5.38 c_mcbond_it 3.4 c_angle_deg 1.7 c_improper_angle_d 1.24 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7875 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 15
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing CNS refinement PDB_EXTRACT data extraction HKL-2000 data collection