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Multi-drug resistant HIV-1 protease 769 variant with reduced LrF peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SO9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 298 0.1 M citric acid and 2.4 M ammonium sulfate at pH 5.2,
VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.1 41.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.294 α = 90 b = 62.294 β = 90 c = 84.049 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 CCD RAYONIX MX-300 2012-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.053 42.02 11642
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.16 97.7
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 3SO9 2.05 42.02 11053 555 99.96 0.19924 0.19588 0.198 0.26319 0.266 RANDOM 20.649
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] 0.77 0.38 0.77 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.421 r_dihedral_angle_4_deg 19.646 r_dihedral_angle_3_deg 17.215 r_dihedral_angle_1_deg 7.403 r_scangle_it 5.152 r_scbond_it 3.169 r_angle_refined_deg 2.038 r_mcangle_it 1.936 r_mcbond_it 1.133 r_chiral_restr 0.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.421 r_dihedral_angle_4_deg 19.646 r_dihedral_angle_3_deg 17.215 r_dihedral_angle_1_deg 7.403 r_scangle_it 5.152 r_scbond_it 3.169 r_angle_refined_deg 2.038 r_mcangle_it 1.936 r_mcbond_it 1.133 r_chiral_restr 0.144 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 1573 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement