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Crystal Structure of HIV-1 Protease (Q7K) in Complex with Atazanavir
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 5.6 298 750 mM NaCl, 100 mM citrate buffer, pH 5.6, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.69 54.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.741 α = 90 b = 85.805 β = 90 c = 46.242 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 2004-06-11 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 1.6 50 98.3 0.051 0.051 13.9 4.6 30983
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 1.6 1.66 95.7 0.472 0.472 2.88 3.8 2968
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 1.6 23.82 30961 3104 98.3 0.186 0.183 0.209 RANDOM 24.304
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] 0.13 -0.09 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.303 r_dihedral_angle_4_deg 13.521 r_dihedral_angle_3_deg 10.52 r_dihedral_angle_1_deg 6.042 r_scangle_it 2.748 r_scbond_it 1.917 r_angle_refined_deg 1.437 r_mcangle_it 1.101 r_mcbond_it 0.781 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.303 r_dihedral_angle_4_deg 13.521 r_dihedral_angle_3_deg 10.52 r_dihedral_angle_1_deg 6.042 r_scangle_it 2.748 r_scbond_it 1.917 r_angle_refined_deg 1.437 r_mcangle_it 1.101 r_mcbond_it 0.781 r_nbtor_refined 0.309 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.157 r_symmetry_hbond_refined 0.148 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1516 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 52
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction