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Crystal structure of the wild-type HIV-1 protease with the inhibitor, Nelfinavir
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 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 2.1 41.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.924 α = 90 b = 57.848 β = 90 c = 61.572 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 1.97 50 98.4 0.049 0.049 22.6 6.1 13251
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 (All) 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 1F7A 1.97 39.25 12557 652 98.33 0.184 0.18627 0.184 0.1968 0.22999 0.238 RANDOM 33.032
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] -1.12 1.63 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.068 r_dihedral_angle_3_deg 13.841 r_dihedral_angle_4_deg 10.493 r_dihedral_angle_1_deg 6.147 r_scangle_it 1.868 r_angle_other_deg 1.641 r_angle_refined_deg 1.327 r_scbond_it 1.224 r_mcangle_it 0.791 r_mcbond_it 0.657
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.068 r_dihedral_angle_3_deg 13.841 r_dihedral_angle_4_deg 10.493 r_dihedral_angle_1_deg 6.147 r_scangle_it 1.868 r_angle_other_deg 1.641 r_angle_refined_deg 1.327 r_scbond_it 1.224 r_mcangle_it 0.791 r_mcbond_it 0.657 r_symmetry_hbond_refined 0.4 r_nbd_other 0.198 r_symmetry_vdw_other 0.187 r_nbd_refined 0.184 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.164 r_mcbond_other 0.123 r_symmetry_vdw_refined 0.092 r_nbtor_other 0.085 r_chiral_restr 0.072 r_gen_planes_other 0.018 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1490 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing