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HIV-1 wild type protease with GRL-02815A, a thiochroman heterocycle with (S)-Boc-amine functionality as the 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 6.4 298 0.90M NaCl, 0.1M Sodium Cacodylate pH 6.4
Crystal Properties Matthews coefficient Solvent content 2.72 54.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.719 α = 90 b = 86.109 β = 90 c = 46.193 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 300 mm CCD 2016-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.2 50 91.1 0.085 20.1 6.9 67382
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.24 52.1 0.37 3.4 2.1
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-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3NU3 1.2 50 67328 67328 3298 91.1 0.1516 0.1498 0.1857 0.1965 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 55 1734.1
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.1034 s_non_zero_chiral_vol 0.0818 s_zero_chiral_vol 0.0747 s_similar_adp_cmpnt 0.049 s_angle_d 0.0317 s_anti_bump_dis_restr 0.0292 s_bond_d 0.0131 s_from_restr_planes 0.0047 s_similar_dist s_rigid_bond_adp_cmpnt
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 48
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing SHELXL refinement