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Crystal Structure of protease inhibitor, MIT-1-AC86 in complex with wild type HIV-1 protease
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 6.2 298 126 mM Sodium Phosphate, 63 mM sodium citrate, 24-29% ammonium sulphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.09 41.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.67 α = 90 b = 57.981 β = 90 c = 61.541 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 200 IMAGE PLATE RIGAKU RAXIS IV osmic mirrors 2005-12-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.85 50 96.9 0.047 4.7 10.9 6.6 15580
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1F7A 1.85 42.18 14764 14764 778 96.91 0.16128 0.16128 0.15936 0.19748 0.2429 RANDOM 20.584
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] -0.78 0.18 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.831 r_dihedral_angle_4_deg 12.635 r_dihedral_angle_3_deg 10.904 r_dihedral_angle_1_deg 6.164 r_scangle_it 1.718 r_angle_refined_deg 1.24 r_scbond_it 1.121 r_mcangle_it 0.703 r_angle_other_deg 0.693 r_mcbond_it 0.485
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.831 r_dihedral_angle_4_deg 12.635 r_dihedral_angle_3_deg 10.904 r_dihedral_angle_1_deg 6.164 r_scangle_it 1.718 r_angle_refined_deg 1.24 r_scbond_it 1.121 r_mcangle_it 0.703 r_angle_other_deg 0.693 r_mcbond_it 0.485 r_symmetry_vdw_other 0.199 r_nbd_refined 0.178 r_nbd_other 0.173 r_nbtor_refined 0.163 r_symmetry_vdw_refined 0.157 r_xyhbond_nbd_refined 0.131 r_symmetry_hbond_refined 0.109 r_mcbond_other 0.104 r_nbtor_other 0.079 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1494 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing