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Structure of HIV-1 Reverse Transcriptase in complex with DNA, dCTP, 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 7.2 277 10-12% PEG 8000, 50 MM BISTRIS-PROPANE PH 7.2, 50 MM AMMONIUM SULFATE, 5% GLYCEROL, 5% SUCROSE
Crystal Properties Matthews coefficient Solvent content 3.08 60.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.663 α = 90 b = 131.247 β = 97.717 c = 137.491 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 PILATUS 6M 2018-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.977 CHESS F1
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 3.14 50 98 0.088 0.097 0.039 0.914 16.2 5.5 53976 56.82
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 3.14 3.2 79.8 0.499 0.59 0.305 0.574 1.5 2.9
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 3.14 34.13 1.41 44328 1998 80.32 0.1962 0.1939 0.1929 0.2437 0.2405 77.46
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 16.802 f_angle_d 0.5822 f_chiral_restr 0.0785 f_plane_restr 0.0033 f_bond_d 0.0024
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15836 Nucleic Acid Atoms 1442 Solvent Atoms 150 Heterogen Atoms 186
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing