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Crystal Structure of Multidrug Resistant HIV-1 Protease Clinical Isolate PR20 in Complex with Amprenavir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UCB PDB ENTRY 3UCB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 298 1.67 M sodium chloride, 67 mM citrate/phosphate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.05 40.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.717 α = 90 b = 65.798 β = 90 c = 93.56 γ = 90
Symmetry Space Group P 21 21 21
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 225 mm CCD mirrors 2009-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.84999 APS 22-BM
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 1.8 50 97.6 0.073 19.3 4.5 17214 16791 2 2
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 1.8 1.86 80 0.468 2.1 3.1
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 (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 THROUGHOUT PDB ENTRY 3UCB 1.8 9.91 17214 15764 828 97.65 0.19015 0.18743 0.1981 0.24279 0.2547 RANDOM 24.471
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] 0.2 -0.05 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.889 r_dihedral_angle_3_deg 14.446 r_dihedral_angle_4_deg 10.208 r_dihedral_angle_1_deg 7.02 r_scangle_it 5.18 r_scbond_it 3.199 r_mcangle_it 2.394 r_angle_refined_deg 2.108 r_mcbond_it 1.427 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.889 r_dihedral_angle_3_deg 14.446 r_dihedral_angle_4_deg 10.208 r_dihedral_angle_1_deg 7.02 r_scangle_it 5.18 r_scbond_it 3.199 r_mcangle_it 2.394 r_angle_refined_deg 2.108 r_mcbond_it 1.427 r_nbtor_refined 0.311 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.168 r_chiral_restr 0.156 r_xyhbond_nbd_refined 0.104 r_symmetry_hbond_refined 0.083 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 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 1518 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 73
Software Software Software Name Purpose SERGUI data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling