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HIV-1 Protease Mutant L76V complexed with Saquinavir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NMY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 298 CRYSTAL WAS GROWN BY THE HANGING-DROP VAPOR-DIFFUSION METHOD AT ROOM TEMPERATURE, FROM A 7 MG/ML PROTEIN SOLUTION AT PH 7.0 WITH 1.3 M NACL, 0.1 M TRIS-HCL, 3% DMSO. THE INHIBITOR WAS MIXED WITH PROTEASE IN A RATIO 5:1, VAPOR DIFFUSION HANGING DROP, TEMPERATURE 298K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.73 54.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.84 α = 90 b = 86.17 β = 90 c = 46.24 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 300 mm CCD 2008-10-09 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 1.45 50 90.1 0.064 27.3 6.6 38308
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 1.45 1.5 56.4 0.48 2.2 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2NMY 1.45 10 38108 1899 90.1 0.148 0.145 0.1542 0.197 0.1924 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 1648 1732.74
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.09 s_non_zero_chiral_vol 0.062 s_zero_chiral_vol 0.052 s_angle_d 0.03 s_from_restr_planes 0.03 s_bond_d 0.01 s_rigid_bond_adp_cmpnt 0.003 s_similar_dist s_anti_bump_dis_restr s_similar_adp_cmpnt
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1510 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 98
Software Software Software Name Purpose MAR345 data collection MOLREP phasing SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling