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Crystal structure of a chemically synthesized 203 amino acid 'covalent dimer' [Gly51;Aib51']HIV-1 protease molecule complexed with MVT-101 reduced isostere inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FSM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.1M citrate, 0.2M sodium phosphate, 30% (w/v) ammonium sulfate, 10% (v/v) DMSO, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.08 40.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.532 α = 90 b = 57.964 β = 90 c = 61.015 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 110 CCD MARMOSAIC 300 mm CCD Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geomet
ry 2006-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97932 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.45 50 92.7 0.083 25.4 6.2 30346
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.5 61.1 0.598 2.46 3.9 3200
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 (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 3FSM 1.45 20 28759 1540 92.5 0.20523 0.20325 0.2074 0.24446 0.2408 RANDOM 22.491
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] -0.13 -0.08 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.811 r_dihedral_angle_4_deg 17.6 r_dihedral_angle_3_deg 13.561 r_dihedral_angle_1_deg 6.88 r_scangle_it 3.757 r_scbond_it 2.539 r_mcangle_it 1.803 r_angle_refined_deg 1.657 r_mcbond_it 1.153 r_angle_other_deg 0.906
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.811 r_dihedral_angle_4_deg 17.6 r_dihedral_angle_3_deg 13.561 r_dihedral_angle_1_deg 6.88 r_scangle_it 3.757 r_scbond_it 2.539 r_mcangle_it 1.803 r_angle_refined_deg 1.657 r_mcbond_it 1.153 r_angle_other_deg 0.906 r_symmetry_hbond_refined 0.335 r_mcbond_other 0.323 r_symmetry_vdw_refined 0.236 r_nbd_refined 0.206 r_nbd_other 0.2 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.155 r_symmetry_vdw_other 0.152 r_chiral_restr 0.099 r_nbtor_other 0.093 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 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 1545 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 54
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling