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Crystal structure of protease inhibitor, MIT-1-KK81 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 2.1 41.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.777 α = 90 b = 58.029 β = 90 c = 61.779 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 2006-02-24 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 50 99.7 0.054 5.4 11.6 6.7 12846
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-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 42.3 12183 12183 625 99.73 0.15861 0.15861 0.1563 0.1693 0.20498 0.2177 RANDOM 22.603
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] -0.5 -0.19 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.669 r_dihedral_angle_4_deg 14.034 r_dihedral_angle_3_deg 10.729 r_dihedral_angle_1_deg 5.828 r_scangle_it 1.514 r_angle_refined_deg 1.211 r_scbond_it 0.994 r_angle_other_deg 0.69 r_mcangle_it 0.686 r_mcbond_it 0.508
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.669 r_dihedral_angle_4_deg 14.034 r_dihedral_angle_3_deg 10.729 r_dihedral_angle_1_deg 5.828 r_scangle_it 1.514 r_angle_refined_deg 1.211 r_scbond_it 0.994 r_angle_other_deg 0.69 r_mcangle_it 0.686 r_mcbond_it 0.508 r_nbd_refined 0.17 r_nbd_other 0.17 r_nbtor_refined 0.164 r_symmetry_vdw_other 0.157 r_xyhbond_nbd_refined 0.135 r_symmetry_hbond_refined 0.128 r_symmetry_vdw_refined 0.107 r_mcbond_other 0.096 r_nbtor_other 0.078 r_chiral_restr 0.076 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 154 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing