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HIV protease wild-type in complex with TMC114 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F7A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 300 1 MG/ML PROTEIN; 5:1 LIGAND:PROTEIN; 30% AMSOR; SODIUM CITRATE AND SODIUM PHOSPHATE, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.1 41.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.746 α = 90 b = 57.807 β = 90 c = 62.006 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 190 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.900 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 95.5 0.038 0.038 25 5.5 55056 55056
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.24 76.2 0.317 0.317 4320
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1F7A 1.2 42.26 55001 52226 2775 95.52 0.14 0.1397 0.179 RANDOM 15.422
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] -0.39 -0.06 0.45
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 16.645 r_sphericity_bonded 9.511 r_scangle_it 8.132 r_dihedral_angle_1_deg 6.96 r_scbond_it 5.811 r_mcangle_it 4.242 r_mcbond_it 3.219 r_rigid_bond_restr 2.59 r_angle_refined_deg 1.593 r_angle_other_deg 0.722
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 16.645 r_sphericity_bonded 9.511 r_scangle_it 8.132 r_dihedral_angle_1_deg 6.96 r_scbond_it 5.811 r_mcangle_it 4.242 r_mcbond_it 3.219 r_rigid_bond_restr 2.59 r_angle_refined_deg 1.593 r_angle_other_deg 0.722 r_symmetry_hbond_refined 0.338 r_symmetry_vdw_other 0.312 r_symmetry_vdw_refined 0.31 r_nbd_other 0.274 r_xyhbond_nbd_refined 0.254 r_nbd_refined 0.244 r_chiral_restr 0.149 r_nbtor_other 0.095 r_bond_refined_d 0.039 r_gen_planes_other 0.028 r_gen_planes_refined 0.021 r_bond_other_d 0.007 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1496 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 63
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement