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Crystal Structure of Wild-type HIV-1 Protease in Complex With TMC310911
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F7A PDB ENTRY 1F7A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 295 24-29% ammonium sulfate, 63 mM sodium citrate, 126 mM phosphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.09 41.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.681 α = 90 b = 58.369 β = 90 c = 61.116 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 193 IMAGE PLATE RIGAKU RAXIS IV 2005-11-09 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 98.6 0.054 13.9 6.6 14669
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 96.5 0.323 5.9 1412
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 1F7A 1.9 42.22 14635 738 98.67 0.1818 0.1794 0.1937 0.2269 0.2458 RANDOM 39.0945
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] -1.49 -0.18 1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.46 r_dihedral_angle_4_deg 21.181 r_dihedral_angle_3_deg 12.179 r_dihedral_angle_1_deg 6.349 r_angle_refined_deg 1.527 r_angle_other_deg 0.808 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.46 r_dihedral_angle_4_deg 21.181 r_dihedral_angle_3_deg 12.179 r_dihedral_angle_1_deg 6.349 r_angle_refined_deg 1.527 r_angle_other_deg 0.808 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1494 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 57
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction AMoRE phasing