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HIV-1 PR mutant in complex with nelfinavir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U8G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 298 reservoir solution: 0.5M (NH4)2SO4, 0.1M MES pH 5.4 or pH 5.5; drops: 2+1ul (protein+reservoir}; protein: 3-5mg/ml 5-fold molar excess of inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.15 42.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.5 α = 90 b = 62.5 β = 90 c = 82.06 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate double mirrors X-ray optical system (Bruker) 2005-03-03 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) 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 2.1 54.15 96.1 0.085 6.3 6.8 9287 -3 38
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 2.1 2.2 96.1 0.411 1.8
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 1U8G 2.2 54.15 8003 881 95.74 0.19074 0.1843 0.1883 0.25005 0.2498 RANDOM 25.116
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] 0.21 0.11 0.21 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.869 r_dihedral_angle_4_deg 17.312 r_dihedral_angle_3_deg 14.934 r_dihedral_angle_1_deg 6.406 r_scangle_it 1.843 r_angle_refined_deg 1.32 r_scbond_it 1.255 r_mcangle_it 0.741 r_mcbond_it 0.499 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.869 r_dihedral_angle_4_deg 17.312 r_dihedral_angle_3_deg 14.934 r_dihedral_angle_1_deg 6.406 r_scangle_it 1.843 r_angle_refined_deg 1.32 r_scbond_it 1.255 r_mcangle_it 0.741 r_mcbond_it 0.499 r_nbtor_refined 0.316 r_symmetry_hbond_refined 0.232 r_symmetry_vdw_refined 0.213 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.076 r_bond_refined_d 0.012 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 1506 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 40
Software Software Software Name Purpose HKL-3000 data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling