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Crystal Structure of HIV-1 Protease Mutant I54M with Antiviral Drug Amprenavir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F8G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 Crystal was grown by the hanging-drop vapor-diffusion method at room temperature, from a 2.2 mg/ml protein solution at pH 4.6 with 0.1M sodium acetate, 0.67M sodium chloride. The inhibitor was mixed with protease in a ratio 5:1 , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.67 54.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.12 α = 90 b = 85.91 β = 90 c = 46.1 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 2007-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 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 1.16 50 91.8 0.072 5 10.6
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) 1.16 1.2 58.9 0.357 2 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-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION AB INITIO FREE R 2F8G 1.16 10 73463 73463 3680 91.6 0.1542 0.1523 0.1523 0.1566 0.1879 0.1834 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 11 1648.37 1765.77
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.101 s_anti_bump_dis_restr 0.089 s_non_zero_chiral_vol 0.077 s_zero_chiral_vol 0.072 s_similar_adp_cmpnt 0.04 s_angle_d 0.033 s_from_restr_planes 0.0289 s_bond_d 0.016 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 47
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling