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Crystal Structure of HIV-1 protease complexed with PL-100
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 295 1:1 protein:reservoir, 6 mg/mL protein, 0.6 mM PL-100, protein buffer: 10 mM MES, 1 mM DTT, 1 mM EDTA, 3 mM NaN3, reservoir: 0.6 M NaCl, 100 mM NaOAc, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.65 53.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.79 α = 90 b = 85.98 β = 90 c = 46.19 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 93 IMAGE PLATE RIGAKU RAXIS HTC Osmic VariMax HR 2006-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 47.96 99.6 0.073 10.6 4.38 21909
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) 1.8 1.86 100 0.323 3.5 4.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 THROUGHOUT 1.8 47.96 20770 1125 99.55 0.20729 0.20502 0.2032 0.24783 0.2463 RANDOM 17.741
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] 0.19 -0.54 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.94 r_dihedral_angle_4_deg 11.721 r_dihedral_angle_3_deg 10.972 r_dihedral_angle_1_deg 5.436 r_scangle_it 2.327 r_scbond_it 1.462 r_angle_refined_deg 1.183 r_mcangle_it 0.897 r_mcbond_it 0.592 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.94 r_dihedral_angle_4_deg 11.721 r_dihedral_angle_3_deg 10.972 r_dihedral_angle_1_deg 5.436 r_scangle_it 2.327 r_scbond_it 1.462 r_angle_refined_deg 1.183 r_mcangle_it 0.897 r_mcbond_it 0.592 r_nbtor_refined 0.302 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.179 r_xyhbond_nbd_refined 0.116 r_symmetry_hbond_refined 0.082 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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 244 Heterogen Atoms 88
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction MOLREP phasing