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Crystal structure analysis of HIV-1 protease mutant I84V with a substrate analog P2-NC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FG6 PDB Entry 1FG6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 293 SODIUM CHLORIDE 0.4M, DMSO 5%, CITRATE PHOSPHATE BUFFER PH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.25 45.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.802 α = 90 b = 85.589 β = 90 c = 46.461 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 ADSC QUANTUM 4 Pt-coated toroidal Si mirror 2002-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C NSLS X26C
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 1.3 50 95.9 0.079 14.4 6.6 57616
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 1.3 1.35 72.4 0.33 3.2 2.9
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R PDB Entry 1FG6 1.3 10 55009 47767 2761 96 0.1264 0.1234 0.1351 0.1659 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 24 1659 1795.26
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.089 s_approx_iso_adps 0.085 s_zero_chiral_vol 0.075 s_similar_adp_cmpnt 0.037 s_from_restr_planes 0.0307 s_angle_d 0.03 s_anti_bump_dis_restr 0.029 s_bond_d 0.013 s_rigid_bond_adp_cmpnt 0.004 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1510 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 83
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data reduction SHELX model building SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling SHELX phasing