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Cystal structure of HIV-1 Active Site Mutant D25N and inhibitor 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 5 295 SODIUM ACETATE BUFFER, 30% SODIUM CHLORIDE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.68 54.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.26 α = 90 b = 85.91 β = 90 c = 46.051 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 MARRESEARCH 2000-11-08 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 1.3 50 89.8 0.062 17.5 4.9 51872 49278 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 1.3 1.35 71.8 0.6 2.2 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 AB INITIO FREE R PDB entry 1DAZ 1.3 10 2 51872 49278 2594 90.3 0.1599 0.15 0.1559 0.21 0.1964 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 22 1635 1697.8
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.092 s_approx_iso_adps 0.09 s_zero_chiral_vol 0.065 s_similar_adp_cmpnt 0.06 s_anti_bump_dis_restr 0.038 s_angle_d 0.033 s_from_restr_planes 0.0291 s_bond_d 0.013 s_rigid_bond_adp_cmpnt 0.004 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 46
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing