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Crystal Structure of HIV-1 Protease (Q7K, I50V) in Complex with Tipranavir
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 298 0.75-1.5 M NaCl, 100 mM citrate buffer pH 5.4-6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.72 54.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.957 α = 90 b = 86.411 β = 90 c = 46.186 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 2004-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 1.008 NSLS X4A
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 1.33 24.35 85 0.077 0.077 17.5 5.8 46728
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 1.33 1.38 88.5 0.397 0.397 5.62 5.1 4770
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 1.33 24.35 46642 4719 84.99 0.193 0.19 0.216 RANDOM 16.639
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] -0.01 -0.05 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.99 r_dihedral_angle_3_deg 10.939 r_dihedral_angle_4_deg 7.585 r_dihedral_angle_1_deg 5.678 r_scangle_it 2.394 r_scbond_it 1.642 r_angle_refined_deg 1.327 r_mcangle_it 1.045 r_mcbond_it 0.716 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.99 r_dihedral_angle_3_deg 10.939 r_dihedral_angle_4_deg 7.585 r_dihedral_angle_1_deg 5.678 r_scangle_it 2.394 r_scbond_it 1.642 r_angle_refined_deg 1.327 r_mcangle_it 1.045 r_mcbond_it 0.716 r_nbtor_refined 0.302 r_nbd_refined 0.185 r_symmetry_vdw_refined 0.124 r_xyhbond_nbd_refined 0.099 r_symmetry_hbond_refined 0.082 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1514 Nucleic Acid Atoms Solvent Atoms 380 Heterogen Atoms 56
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling