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Crystal Structure of wild-type HIV protease in complex with the inhibitor, Atazanavir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F7A PDB ENTRY 1F7A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 300 126mM Sodium Phosphate pH 6.2; 63mM sodium citrate; 24-29% ammonium sulphate
, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.12 41.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.862 α = 90 b = 58.099 β = 90 c = 61.999 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 200 IMAGE PLATE RIGAKU RAXIS IV Yale mirrors M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.8 50 95.7 0.071 0.071 8.9 6.8 16904
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1F7A 1.8 42.41 16003 861 95.65 0.17739 0.17566 0.1904 0.20857 0.2168 RANDOM 17.92
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] 0.08 0.26 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.034 r_dihedral_angle_4_deg 14.01 r_dihedral_angle_3_deg 11.552 r_dihedral_angle_1_deg 5.896 r_scangle_it 1.53 r_angle_refined_deg 1.179 r_scbond_it 1.026 r_angle_other_deg 0.704 r_mcangle_it 0.596 r_mcbond_it 0.431
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.034 r_dihedral_angle_4_deg 14.01 r_dihedral_angle_3_deg 11.552 r_dihedral_angle_1_deg 5.896 r_scangle_it 1.53 r_angle_refined_deg 1.179 r_scbond_it 1.026 r_angle_other_deg 0.704 r_mcangle_it 0.596 r_mcbond_it 0.431 r_symmetry_vdw_refined 0.281 r_nbd_refined 0.181 r_nbd_other 0.173 r_nbtor_refined 0.164 r_symmetry_vdw_other 0.163 r_symmetry_hbond_refined 0.138 r_xyhbond_nbd_refined 0.125 r_mcbond_other 0.101 r_nbtor_other 0.077 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1502 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing