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Crystal Structure of HIV-1 Protease Mutant I84V 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 4 298 Crystal was grown by the hanging-drop vapor-diffusion method at room temperature, from a 2.2 mg/ml protein solution at pH 4.0 with 0.13M NaI, 0.1M NaOAc. The inhibitor was mixed with protease in a ratio 5:1 , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.74 55.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.513 α = 90 b = 86.881 β = 90 c = 45.448 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 2008-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 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 1.85 50 93.2 0.097 4 19.6
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) 1.85 1.9 76.6 0.345 2.7 3.6 1552
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2F8G 1.85 9.97 949 93.09 0.20066 0.20066 0.19884 0.23555 0.2512 RANDOM 27.34
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] 0.06 0.09 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.662 r_dihedral_angle_4_deg 13.447 r_dihedral_angle_3_deg 12.564 r_dihedral_angle_1_deg 5.959 r_scangle_it 4.302 r_scbond_it 2.522 r_angle_refined_deg 1.546 r_mcangle_it 1.456 r_mcbond_it 0.841 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.662 r_dihedral_angle_4_deg 13.447 r_dihedral_angle_3_deg 12.564 r_dihedral_angle_1_deg 5.959 r_scangle_it 4.302 r_scbond_it 2.522 r_angle_refined_deg 1.546 r_mcangle_it 1.456 r_mcbond_it 0.841 r_nbtor_refined 0.312 r_nbd_refined 0.192 r_xyhbond_nbd_refined 0.191 r_symmetry_vdw_refined 0.17 r_symmetry_hbond_refined 0.107 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1510 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 65
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling