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Crystal Structure of HIV-1 Protease Mutant N88D with novel P1'-Ligands GRL-02031
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H5B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.2 298 NaCl/sodium acetate buffer at pH 4.2 The concentration of protein is no higher than 3 mg/ml. The ratio for protein/inhibitor is 1:5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.32 54.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.255 α = 90 b = 86.386 β = 90 c = 46.068 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 2009-03-27 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 1.55 50 99.5 0.075 23.2 7.1 34554
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 1.55 1.61 99.9 0.425 4.2 6.3
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 3H5B 1.55 10 34309 1712 99.9 0.1609 0.1578 0.1527 0.2156 0.2025 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 9 1635 1690
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.071 s_similar_adp_cmpnt 0.057 s_non_zero_chiral_vol 0.05 s_zero_chiral_vol 0.043 s_from_restr_planes 0.0283 s_angle_d 0.028 s_anti_bump_dis_restr 0.026 s_bond_d 0.009 s_rigid_bond_adp_cmpnt 0.003 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 63
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling