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HIV-1 protease triple mutants V32I, I47V, V82I with GRL-011-11A (a methylamine bis-Tetrahydrofuran P2-Ligand, sulfonamide isostere derivate)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NU3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 The protein (about 5 mg/mL) was preincubated with the inhibitor (dissolved in dimethylsulfoxide) at a molar ratio of 1:5. Crystals were grown from 0.1 m sodium acetate buffer, pH 4.6 and 2M NaCl as precipitant. Crystals were cryo-cooled in liquid nitrogen after soaking in 30% glycerol to prevent freezing.
Crystal Properties Matthews coefficient Solvent content 2.73 54.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.574 α = 90 b = 86.517 β = 90 c = 46.322 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2017-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
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 1.5 50 96.8 0.059 0.064 0.024 0.998 26.6 6.7 37188 17.7
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 1.5 1.55 76.4 0.493 0.569 0.278 0.803 3.1 4.1
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 3NU3 1.5 33.52 35326 1818 96.75 0.13356 0.13158 0.1321 0.17132 0.1729 RANDOM 19.383
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] 0.48 -0.05 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.757 r_dihedral_angle_3_deg 13.536 r_dihedral_angle_4_deg 8.495 r_dihedral_angle_1_deg 7.001 r_scangle_other 5.108 r_long_range_B_other 4.743 r_long_range_B_refined 4.742 r_scbond_it 4.598 r_scbond_other 4.573 r_rigid_bond_restr 4.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.757 r_dihedral_angle_3_deg 13.536 r_dihedral_angle_4_deg 8.495 r_dihedral_angle_1_deg 7.001 r_scangle_other 5.108 r_long_range_B_other 4.743 r_long_range_B_refined 4.742 r_scbond_it 4.598 r_scbond_other 4.573 r_rigid_bond_restr 4.247 r_mcangle_other 3.316 r_mcangle_it 3.311 r_mcbond_other 2.597 r_mcbond_it 2.596 r_angle_refined_deg 2.242 r_angle_other_deg 1.437 r_chiral_restr 0.261 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1514 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing