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Crystal structure of wild-type HIV-1 protease with novel tricyclic P2-ligands GRL-0739A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NU3 PDB ENTRY 3NU3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 1.15 M NaCl + 0.1 M Na acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.32 54.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.477 α = 90 b = 86.3 β = 90 c = 46.045 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 2012-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM APS 22-BM
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 1.29 50 92.6 0.061 21.9 6.5 56283 56283 13.2
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 1.29 1.34 54.7 0.436 2 2.5 3275
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 PDB ENTRY 3NU3 1.29 10 55418 55418 2770 93.5 0.1416 0.1394 0.1394 0.1487 0.1799 0.1773 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 25 1645 1741.25
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.082 s_non_zero_chiral_vol 0.071 s_zero_chiral_vol 0.07 s_similar_adp_cmpnt 0.052 s_angle_d 0.032 s_from_restr_planes 0.0295 s_anti_bump_dis_restr 0.028 s_bond_d 0.013 s_rigid_bond_adp_cmpnt 0.004 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 70
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling