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Crystal structure of wild-type HIV-1 Reverse Transcriptase crosslinked to a DSDNA with a bound excision product, AZTPPPPA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RTD PDB ENTRY 1RTD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.8 50 MM BIS-TRIS PROPANE PH6.4, 10-11% PEG8000, 0.3 M (NH4)2SO4, 5% GLYCEROL, 5% SUCROSE,
20 MM MGCL2, AND 5 MM SPERMIDINE, PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.0K
Crystal Properties Matthews coefficient Solvent content 3.14 60.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.529 α = 90 b = 274.806 β = 90.11 c = 152.371 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 CCD ADSC QUANTUM 210 2006-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 CHESS A1
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 3.15 25 90.3 0.129 5.3 98589
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) 3.15 3.21 83.5 0.539 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1RTD 3.15 24.83 98356 1978 88.6 0.264 0.264 0.2598 0.288 0.2849 RANDOM 72.7
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 c_dihedral_angle_d 22.8 c_angle_deg 1.4 c_improper_angle_d 1.11 c_bond_d 0.01 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 22.8 c_angle_deg 1.4 c_improper_angle_d 1.11 c_bond_d 0.01 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 31616 Nucleic Acid Atoms 3516 Solvent Atoms 76 Heterogen Atoms 232
Software Software Software Name Purpose ADSC data collection PHASER phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling