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HIV-1 wild Type protease with GRL-1118A , an isophthalamide-derived P2-P3 ligand with the 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 4.8 298 1.28 M NaCl, 0.1 M Sodium Acetate, pH 4.8
Crystal Properties Matthews coefficient Solvent content 2.69 54.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.179 α = 90 b = 86.515 β = 90 c = 45.945 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 1.0 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 1.33 50 96.2 0.072 18.2 6.5 52049
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 1.33 1.38 72.4 0.456 2.2 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R 3DJK 1.33 50 51979 2602 96.2 0.154 0.1524 0.1373 0.1834 0.1693 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 38 1706.85
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.082 s_non_zero_chiral_vol 0.08 s_zero_chiral_vol 0.066 s_similar_adp_cmpnt 0.056 s_from_restr_planes 0.0298 s_angle_d 0.029 s_anti_bump_dis_restr 0.018 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 182 Heterogen Atoms 49
Software Software Software Name Purpose SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing