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Crystal structure of protease inhibitor, MIT-2-KB98 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 41.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.907 α = 90 b = 58.258 β = 90 c = 61.81 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 2006-09-20 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 92.5 0.044 4.4 21.4 5 15105
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 1.85 42.41 14314 14314 766 92.61 0.17252 0.17252 0.17047 0.1826 0.21213 0.2231 RANDOM 17.29
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] -0.63 -0.01 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.517 r_dihedral_angle_4_deg 15.794 r_dihedral_angle_3_deg 10.672 r_dihedral_angle_1_deg 5.946 r_scangle_it 1.617 r_angle_refined_deg 1.253 r_scbond_it 1.057 r_mcangle_it 0.754 r_angle_other_deg 0.714 r_mcbond_it 0.543
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.517 r_dihedral_angle_4_deg 15.794 r_dihedral_angle_3_deg 10.672 r_dihedral_angle_1_deg 5.946 r_scangle_it 1.617 r_angle_refined_deg 1.253 r_scbond_it 1.057 r_mcangle_it 0.754 r_angle_other_deg 0.714 r_mcbond_it 0.543 r_nbd_refined 0.18 r_nbd_other 0.173 r_nbtor_refined 0.166 r_symmetry_vdw_other 0.163 r_symmetry_vdw_refined 0.135 r_symmetry_hbond_refined 0.135 r_xyhbond_nbd_refined 0.128 r_mcbond_other 0.117 r_nbtor_other 0.079 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 146 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing