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Crystal Structure of HIV-1 Protease (Q7K, L33I, L63I) in Complex with KNI-10074
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MSM PDB ENTRY 1MSM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 citrate buffer pH 7.2, 100 mM DTT, 3mM NaN3 and 750 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.69 54.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.31 α = 90 b = 86.095 β = 90 c = 46.369 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 2008-07-16 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 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 2.2 48.3 99.8 0.12 11.2 4.4 12408
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 100 0.46 2.9 4.4 1212
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1MSM 2.2 48.28 11781 597 99.81 0.17987 0.17703 0.1857 0.23743 0.243 RANDOM 22.917
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] -0.58 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.113 r_dihedral_angle_4_deg 13.594 r_dihedral_angle_3_deg 13.396 r_dihedral_angle_1_deg 5.182 r_angle_refined_deg 1.238 r_scangle_it 1.186 r_scbond_it 0.74 r_mcangle_it 0.431 r_nbtor_refined 0.301 r_mcbond_it 0.272
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.113 r_dihedral_angle_4_deg 13.594 r_dihedral_angle_3_deg 13.396 r_dihedral_angle_1_deg 5.182 r_angle_refined_deg 1.238 r_scangle_it 1.186 r_scbond_it 0.74 r_mcangle_it 0.431 r_nbtor_refined 0.301 r_mcbond_it 0.272 r_nbd_refined 0.181 r_symmetry_vdw_refined 0.128 r_xyhbond_nbd_refined 0.125 r_symmetry_hbond_refined 0.091 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1516 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 55
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling