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Crystal structure of wild type HIV-1 protease with macrocyclic inhibitor GRL-0216A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B7V PDB entry 3B7V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 Protein solution: 1:15 molar ratio of protease at 2.0 mg/mL and inhibitor GRL-0216A dissolved in dimethylsulfoxide (DMSO). Reservoir solution: 5% Glycerol, 0.5 M NaI in 0.2 M MES buffer, pH 6.0. Crystal mounted on a nylon loop in the liquid nitrogen with additional 28% v/v Glycerol as cryoprotectant, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.71 54.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.764 α = 90 b = 86.328 β = 90 c = 45.976 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 90 CCD MARMOSAIC 300 mm CCD 2007-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.8000 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 1.17 50 90 0.108 14.7 6.5 72239 72239 11.8
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 1.17 1.21 52.6 0.457 2.4 3.3 4137
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R PDB entry 3B7V 1.17 10 72049 72049 3607 90.9 0.1614 0.1614 0.1594 0.1957 0.1953 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 26 1602 1722.65
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.091 s_zero_chiral_vol 0.08 s_non_zero_chiral_vol 0.075 s_similar_adp_cmpnt 0.035 s_angle_d 0.034 s_from_restr_planes 0.0309 s_anti_bump_dis_restr 0.03 s_bond_d 0.014 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 181 Heterogen Atoms 77
Software Software Software Name Purpose MAR345 data collection PHASER phasing SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling