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Crystal Structure of HIV-1 RT in Complex with NBD-14189
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G1Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 277 10% PEG 8,000, 4% PEG 400, 100 mM imidazole pH 6.6,10 mM spermine, 15 mM MgSO4,100 mM (NH4)2SO4, and 5 mM tris(2-carboxyethyl)phosphine(TCEP)
Crystal Properties Matthews coefficient Solvent content 2.84 56.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.433 α = 90 b = 72.953 β = 99.874 c = 107.747 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 2020-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.96868 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 2.316 34.82 99.1 0.071 0.077 0.03 0.996 23.6 5.9 53283 63.7
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 2.316 2.35 90.3 0.58 0.67 0.33 0.49 2 3.6
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 4G1Q 2.32 34.82 1.38 53253 2000 98.74 0.2159 0.2146 0.2161 0.2482 0.2486 92.28
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 19.972 f_angle_d 0.8741 f_chiral_restr 0.1611 f_bond_d 0.0058 f_plane_restr 0.0051
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7921 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 65
Software Software Software Name Purpose HKL-2000 data reduction PHENIX refinement HKL-2000 data scaling PHASER phasing