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Crystal Structure of HIV-1 Protease (Q7K, L33I, L63I) in Complex with KNI-10033
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MSM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 100 MES pH 6.5, 500 mM NaCl, 10 mM DTT, 3 mM NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.71 54.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.436 α = 90 b = 85.99 β = 90 c = 46.596 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 IMAGE PLATE RIGAKU RAXIS IV Osmic Mirrors 2005-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 33.54 97.4 0.054 0.054 12.5 3.7 41430
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.5 96.3 0.806 0.806 1.73 3.6 4071
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1MSM 1.45 33.54 41398 4159 97.22 0.207 0.204 0.228 RANDOM 20.527
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] 0.14 -0.05 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.107 r_dihedral_angle_3_deg 12.245 r_dihedral_angle_4_deg 10.533 r_dihedral_angle_1_deg 5.916 r_scangle_it 3.297 r_scbond_it 2.291 r_angle_refined_deg 1.83 r_mcangle_it 1.643 r_mcbond_it 1.055 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.107 r_dihedral_angle_3_deg 12.245 r_dihedral_angle_4_deg 10.533 r_dihedral_angle_1_deg 5.916 r_scangle_it 3.297 r_scbond_it 2.291 r_angle_refined_deg 1.83 r_mcangle_it 1.643 r_mcbond_it 1.055 r_nbtor_refined 0.319 r_nbd_refined 0.225 r_symmetry_vdw_refined 0.161 r_symmetry_hbond_refined 0.136 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.12 r_bond_refined_d 0.016 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1516 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 60
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing