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Crystal Structure of HIV-1 Protease (Q7K, L33I, L63I ) in Complex with KNI-10075
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 5.4 298 100 mM citrate buffer pH 5.4, NaCl 750 mM, 10 mM DTT, 3 mM NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 298KK
Crystal Properties Matthews coefficient Solvent content 2.7 54.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.842 α = 90 b = 85.991 β = 90 c = 46.21 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 315 2004-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.10 NSLS X25
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 1.9 50 99.8 0.113 0.113 14.2 6 19013
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 1.9 1.97 99.9 0.415 0.415 8.63 5.9 1856
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 1.9 48.56 18976 1940 99.72 0.164 0.16 0.2 RANDOM 23.898
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] -0.26 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.089 r_dihedral_angle_4_deg 16.876 r_dihedral_angle_3_deg 11.633 r_dihedral_angle_1_deg 6.276 r_scangle_it 3.166 r_scbond_it 2.183 r_angle_refined_deg 1.591 r_mcangle_it 1.294 r_mcbond_it 0.952 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.089 r_dihedral_angle_4_deg 16.876 r_dihedral_angle_3_deg 11.633 r_dihedral_angle_1_deg 6.276 r_scangle_it 3.166 r_scbond_it 2.183 r_angle_refined_deg 1.591 r_mcangle_it 1.294 r_mcbond_it 0.952 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.222 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.161 r_symmetry_hbond_refined 0.108 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1516 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 62
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing