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Crystal structure of protease inhibitor, MIT-1-KK80 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 2.12 41.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.975 α = 90 b = 58.242 β = 90 c = 61.701 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 2006-02-23 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 2.1 50 99 0.051 5.1 10.7 6.9 11126
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 (All) 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 2.1 42.37 10563 530 99.03 0.17307 0.17307 0.17034 0.1811 0.2302 0.2367 RANDOM 30.983
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] -0.71 0.17 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.691 r_dihedral_angle_3_deg 13.17 r_dihedral_angle_4_deg 13.139 r_dihedral_angle_1_deg 6.855 r_scangle_it 2.534 r_scbond_it 1.626 r_angle_refined_deg 1.267 r_mcangle_it 1.018 r_mcbond_it 0.718 r_angle_other_deg 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.691 r_dihedral_angle_3_deg 13.17 r_dihedral_angle_4_deg 13.139 r_dihedral_angle_1_deg 6.855 r_scangle_it 2.534 r_scbond_it 1.626 r_angle_refined_deg 1.267 r_mcangle_it 1.018 r_mcbond_it 0.718 r_angle_other_deg 0.65 r_nbd_other 0.192 r_nbd_refined 0.182 r_mcbond_other 0.178 r_symmetry_vdw_other 0.174 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.153 r_symmetry_hbond_refined 0.144 r_symmetry_vdw_refined 0.127 r_nbtor_other 0.083 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 1490 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing