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Effect of Flap Mutations on Structure of HIV-1 Protease and Inhibition by Saquinavir and Darunavir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DAZ PDB entry 1DAZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 295 CITRATE/PHOSPHATE BUFFER, KCl, 1.3M, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.67 53.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.16 α = 90 b = 86.25 β = 90 c = 45.92 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD MARMOSAIC 300 mm CCD 2006-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
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 1.4 50 82.1 0.094 13.2 3.5 40435 33211 4 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 1.4 1.45 55.8 0.203 2 1.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 FREE R PDB entry 1DAZ 1.4 10 40435 33211 2022 82.1 0.1688 0.16 0.1548 0.2342 0.2116 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 12 1649 1737.3
RMS Deviations Key Refinement Restraint Deviation s_anti_bump_dis_restr 0.272 s_approx_iso_adps 0.086 s_non_zero_chiral_vol 0.061 s_similar_adp_cmpnt 0.059 s_zero_chiral_vol 0.051 s_angle_d 0.029 s_from_restr_planes 0.029 s_bond_d 0.011 s_rigid_bond_adp_cmpnt 0.003 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1518 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 49
Software Software Software Name Purpose AMoRE phasing SHELXL-97 refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling