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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 2.17 43.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.402 α = 90 b = 62.402 β = 90 c = 83.099 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 CCD MAR CCD 165 mm double crystal monochromator 2005-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 0.98 ESRF BM16
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 1.85 30 98.8 0.057 6.2 7.2 14745 22.2
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 1.85 1.9 96.2 0.294 2.5
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 1.85 30 14745 768 98.82 0.18993 0.18743 0.1895 0.23809 0.2362 RANDOM 33.68
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] -0.05 -0.03 -0.05 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.448 r_dihedral_angle_3_deg 12.565 r_dihedral_angle_4_deg 9.83 r_dihedral_angle_1_deg 5.898 r_scangle_it 2.229 r_scbond_it 1.423 r_angle_refined_deg 1.299 r_mcangle_it 0.999 r_mcbond_it 0.602 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.448 r_dihedral_angle_3_deg 12.565 r_dihedral_angle_4_deg 9.83 r_dihedral_angle_1_deg 5.898 r_scangle_it 2.229 r_scbond_it 1.423 r_angle_refined_deg 1.299 r_mcangle_it 0.999 r_mcbond_it 0.602 r_nbtor_refined 0.313 r_symmetry_hbond_refined 0.197 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.157 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.094 r_bond_refined_d 0.01 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 1508 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling