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Crystal Structure of HIV-1 Protease Mutant V32I with Antiviral Drug Amprenavir
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 5.4 298 The vapour diffusion, hanging drop method is applied. Amprenvir was dissolved in DMSO. Protein concentration is 2.2 mg/ml. The ratio of inhibitor to protein is 5:1 in 0.1 M sodium acetate buffer (ph=5.4), with 0.4M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.68 54.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.769 α = 90 b = 86.13 β = 90 c = 46.284 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 2007-03-15 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 1.2 50 91.6 0.081 6.1 66626 66626 12.517
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) 1.2 1.24 62.7 0.442 2.5 3.4 4482
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3NU3 1.2 10 3326 91.6 0.1639 0.1619 0.1619 0.1651 0.2002 0.1956 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 15 1637 1674.81
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.08 s_non_zero_chiral_vol 0.076 s_zero_chiral_vol 0.068 s_similar_adp_cmpnt 0.038 s_angle_d 0.031 s_from_restr_planes 0.0293 s_anti_bump_dis_restr 0.029 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 150 Heterogen Atoms 39
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling