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HIV-1 wild Type protease with GRL-0518A , an isophthalamide-derived P2-P3 ligand with the para-hydoxymethyl sulfonamide isostere as the P2' group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DJK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 1.24 M NaCl, 0.1 M Sodium Acetate, pH 5.0
Crystal Properties Matthews coefficient Solvent content 2.68 54.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.175 α = 90 b = 86.418 β = 90 c = 45.828 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 100 CCD MARMOSAIC 225 mm CCD 2008-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1 APS 22-BM
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 1.27 50 91.8 0.054 26.5 6.2 57235
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 1.27 1.32 51 0.351 2.2 2
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3DJK 1.27 50 56943 2845 92.3 0.1471 0.1445 0.198 0.1806 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 60 1761.95
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.085 s_approx_iso_adps 0.084 s_zero_chiral_vol 0.068 s_similar_adp_cmpnt 0.051 s_from_restr_planes 0.0308 s_angle_d 0.03 s_anti_bump_dis_restr 0.014 s_bond_d 0.012 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 281 Heterogen Atoms 47
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing SHELXL-97 refinement