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HIV-1 protease triple mutants V32I, I47V, V82I with antiviral drug amprenavir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DJK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 298 FROM A 3.5MG/ML PROTEIN SOLUTION AT PH 5.4 WITH 0.175M KI, 0.1M CITRATE PHOSPHATE, 4% DMSO. 1.0ul WELL SOLUTION WITH 1.5ul PROTEIN SOLUTION. THE INHIBITOR WAS MIXED WITH PROTEASE IN A RATIO 5:1, EVAPORATION, TEMPERATURE 298K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.72 54.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.374 α = 90 b = 86.565 β = 90 c = 46.306 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 2008-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.8 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 1.26 50 91.3 0.063 14.5 3.7 58771 58771 14.8
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 1.26 1.31 59.9 0.361 2.1 2 3786
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R 3DJK 1.26 10 58559 58559 2926 91.5 0.1623 0.1602 0.1602 0.2002 0.1722 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 21 1635 1662.6
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.078 s_non_zero_chiral_vol 0.064 s_zero_chiral_vol 0.063 s_similar_adp_cmpnt 0.058 s_angle_d 0.031 s_from_restr_planes 0.028 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 1514 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 64
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling