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Structure of HIV-1 Reverse Transcriptase in complex with a DNA aptamer, AZTTP, and CA(2+) ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D3G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 7% PEG 8000, 25 MM BISTRIS-PROPANE PH 6.8, 75 MM BISTRIS-PROPANE PH 7.4, 50 MM AMMONIUM SULFATE, 5% GLYCEROL, 5% SUCROSE
Crystal Properties Matthews coefficient Solvent content 3.26 62.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.151 α = 90 b = 132.192 β = 97.15 c = 139.658 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 PIXEL DECTRIS PILATUS3 6M 2014-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.3 50 94.5 0.051 0.058 0.028 11.5 3.7 46338 105.27
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 3.3 3.36 64 0.339 2.5
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 5D3G 3.3 48.449 1.4 46295 1890 94.43 0.2217 0.2206 0.2207 0.2473 0.2485
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 15.595 f_angle_d 0.628 f_chiral_restr 0.044 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15816 Nucleic Acid Atoms 1440 Solvent Atoms Heterogen Atoms 64
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing