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Crystal structure of wild type HIV-1 protease with novel P1'-ligand GRL-02031
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DJK PDB entry 3DJK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 Inhibitor GRL-02031 was dissolved in dimethylsulfoxide (DMSO). Crystals were grown using 1:5 molar ratio of protease (at 3.9 mg/ml) to inhibitor. The reservoir contained 0.1 M citrate phosphate buffer, pH 5.0, 0.35 M NaCl and 4% DMSO. Crystals were mounted on a nylon loop and flash-frozen in liquid nitrogen with a cryoprotectant of 30% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.69 54.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.111 α = 90 b = 86.416 β = 90 c = 45.97 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 IMAGE PLATE MAR scanner 300 mm plate 2008-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.8000 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 1.29 50 92.5 0.055 27 6.6 54628 54628 13.5
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 64.3 0.491 2.27 3.9 3723
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 3DJK 1.29 10 54428 54428 2726 92.5 0.1436 0.1436 0.1416 0.1485 0.1813 0.1802 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 18 1638 1720.05
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.087 s_non_zero_chiral_vol 0.071 s_zero_chiral_vol 0.062 s_similar_adp_cmpnt 0.054 s_angle_d 0.031 s_from_restr_planes 0.028 s_anti_bump_dis_restr 0.024 s_bond_d 0.012 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 205 Heterogen Atoms 51
Software Software Software Name Purpose MAR345 data collection AMoRE phasing SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling