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Crystal Structure of a highly resistant HIV-1 protease Clinical isolate PR10x with GRL-0519 (tris-tetrahydrofuran as P2 ligand)
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 5.2 298 Hanging-drop vapor diffusion using equal volumes of protein stock (3.9 mg/mL) and well reservoir solution. Cryoprotected in 30% glycerol. Complex on ice at 1:8 ratio of PR to PI, crystallized in 1 M NaCl and 0.1 M sodium acetate pH 5.2
Crystal Properties Matthews coefficient Solvent content 2.5 57.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.659 α = 90 b = 56.659 β = 90 c = 78.155 γ = 90
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 RAYONIX MX300HE 2017-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.25 50 99.4 0.08 0.086 0.033 20.7 6.8 67583
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 1.25 1.29 97 0.389 0.078 0.03 0.991 3.1 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FREE R-VALUE 3NU3 1.25 50 67583 67540 3385 99.4 0.1479 0.1479 0.1457 0.1653 0.1864 0.1757 RANDOM 20.3406
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 s_approx_iso_adps 0.092 s_non_zero_chiral_vol 0.086 s_zero_chiral_vol 0.08 s_similar_adp_cmpnt 0.052 s_angle_d 0.035 s_from_restr_planes 0.034 s_anti_bump_dis_restr 0.02 s_bond_d 0.013 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1522 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 92
Software Software Software Name Purpose HKL-2000 data scaling MOLREP phasing SHELX refinement PDB_EXTRACT data extraction HKL-2000 data reduction