☰ Navigation Tabs
Crystal Structure of HIV-1 Reverse Transcriptase in Complex with 3-(2-(2-(3-acryloyl-2-oxo-2,3-dihydro-1H-benzo[d]imidazol-1-yl)ethoxy)-4-chlorophenoxy)-5-chlorobenzonitrile (JLJ744), a non-nucleoside inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6X4C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 277 50 mM Imidazole pH 6.3, 14% PEG 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, and 5 mM spermine
Crystal Properties Matthews coefficient Solvent content 3.07 59.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.404 α = 90 b = 73.185 β = 97.51 c = 171.583 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 EIGER X 9M 2022-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9201 NSLS-II 17-ID-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 2.99 170.11 99.7 0.094 0.127 0.067 0.997 8.6 3.6 56302
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 2.991 3.043 1.157 1.597 1.513 0.318
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.99 170.11 53483 2748 99.6 0.223 0.22 0.2634 0.279 0.275 RANDOM 94.19
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] 0.06 0.99 -0.17 -0.15
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 20.017 r_long_range_B_refined 20.016 r_dihedral_angle_3_deg 18.092 r_scangle_other 15.578 r_mcangle_it 14.899 r_mcangle_other 14.898 r_scbond_it 9.883 r_scbond_other 9.882 r_mcbond_it 9.688 r_mcbond_other 9.688
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 20.017 r_long_range_B_refined 20.016 r_dihedral_angle_3_deg 18.092 r_scangle_other 15.578 r_mcangle_it 14.899 r_mcangle_other 14.898 r_scbond_it 9.883 r_scbond_other 9.882 r_mcbond_it 9.688 r_mcbond_other 9.688 r_dihedral_angle_2_deg 8.67 r_dihedral_angle_1_deg 7.756 r_angle_refined_deg 1.37 r_angle_other_deg 0.465 r_chiral_restr 0.057 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13980 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing