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Crystal structure of HIV-1 reverse transcriptase with a double stranded DNA in complex with fragment 048 at the transient P-pocket.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AMO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 11-12% v/v PEG Smear Broad, 10% w/v sucrose, 50 mM PIPES-NaOH pH 6.5, 0.1 M (NH4)2SO4, 5 mM MgCl2, 5 mM CdCl2
Crystal Properties Matthews coefficient Solvent content 3.13 60.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 309.565 α = 90 b = 61.9 β = 104.55 c = 168.779 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 PIXEL DECTRIS PILATUS 6M-F 2019-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91589 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 98.75 94.6 0.323 0.377 0.189 0.973 3.3 3.4 44516 63.17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.42 95.3 0.953 1.104 0.544 0.251 1.4 3.5
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 THROUGHOUT 6AMO 3.3 81.68 1.33 44498 2249 93.79 0.2634 0.2617 0.2616 0.2964 0.2954 63.6493
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15770 Nucleic Acid Atoms 1760 Solvent Atoms Heterogen Atoms 46
Software Software Software Name Purpose iMOSFLM data reduction Aimless data scaling PDB_EXTRACT data extraction PHENIX refinement PHASER phasing Coot model building