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Crystal structure of protease inhibitor, MIT-2-AD93 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 2.11 41.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.855 α = 90 b = 58.178 β = 90 c = 61.804 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 2006-09-14 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 1.8 50 94.5 0.042 4.2 16.6 6.4 16632
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 1.8 42.37 15748 15748 849 94.61 0.17418 0.17418 0.17267 0.1848 0.20317 0.213 RANDOM 16.911
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] -0.55 0.06 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.796 r_dihedral_angle_4_deg 17.885 r_dihedral_angle_3_deg 11.8 r_dihedral_angle_1_deg 6.189 r_scangle_it 1.458 r_angle_refined_deg 1.193 r_scbond_it 0.994 r_angle_other_deg 0.696 r_mcangle_it 0.659 r_mcbond_it 0.549
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.796 r_dihedral_angle_4_deg 17.885 r_dihedral_angle_3_deg 11.8 r_dihedral_angle_1_deg 6.189 r_scangle_it 1.458 r_angle_refined_deg 1.193 r_scbond_it 0.994 r_angle_other_deg 0.696 r_mcangle_it 0.659 r_mcbond_it 0.549 r_nbd_other 0.19 r_nbd_refined 0.176 r_nbtor_refined 0.165 r_symmetry_vdw_other 0.163 r_xyhbond_nbd_refined 0.14 r_symmetry_vdw_refined 0.122 r_symmetry_hbond_refined 0.099 r_mcbond_other 0.089 r_nbtor_other 0.08 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_bond_other_d 0.006 r_gen_planes_refined 0.004 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 1498 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing