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Crystal structure of a chemically synthesized [D25N]HIV-1 protease molecule complexed with MVT-101 reduced isostere inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.1 M 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 2.12 41.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.09 α = 90 b = 57.697 β = 90 c = 61.832 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 ADSC QUANTUM 315 2008-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.00000 APS 21-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 1.3 50 99.8 0.055 32.97 5.9 45790
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 1.3 1.35 98.6 0.375 3.36 3.1 4507
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.3 20 43280 2303 99.44 0.1795 0.17801 0.1872 0.20786 0.2153 RANDOM 12.869
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] -0.19 0.06 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.077 r_dihedral_angle_4_deg 17.327 r_dihedral_angle_3_deg 12.172 r_dihedral_angle_1_deg 6.668 r_scangle_it 4.826 r_sphericity_bonded 4.623 r_scbond_it 4.069 r_rigid_bond_restr 3.351 r_mcangle_it 2.464 r_mcbond_it 1.783
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.077 r_dihedral_angle_4_deg 17.327 r_dihedral_angle_3_deg 12.172 r_dihedral_angle_1_deg 6.668 r_scangle_it 4.826 r_sphericity_bonded 4.623 r_scbond_it 4.069 r_rigid_bond_restr 3.351 r_mcangle_it 2.464 r_mcbond_it 1.783 r_angle_refined_deg 1.697 r_mcbond_other 1.105 r_angle_other_deg 0.935 r_nbd_other 0.206 r_nbd_refined 0.198 r_symmetry_vdw_other 0.183 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.139 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.104 r_symmetry_vdw_refined 0.094 r_nbtor_other 0.089 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1518 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 64
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling