3I2L

Crystal structure of a chemically synthesized [allo-Ile50/50']HIV-1 protease molecule complexed with MVT-101 reduced isostere inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62930.1 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 coefficientSolvent content
2.1242.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.139α = 90
b = 58.084β = 90
c = 61.525γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 3152008-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.97918APS24-ID-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.54099.70.05223.525.930023
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5399.90.4573.165.91476

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.52028442152099.70.20190.200010.23872RANDOM17.76
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]
0.18-0.250.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.936
r_dihedral_angle_4_deg20.356
r_dihedral_angle_3_deg14.242
r_dihedral_angle_1_deg6.207
r_scangle_it3.497
r_scbond_it2.415
r_angle_refined_deg1.663
r_mcangle_it1.637
r_mcbond_it1.108
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.936
r_dihedral_angle_4_deg20.356
r_dihedral_angle_3_deg14.242
r_dihedral_angle_1_deg6.207
r_scangle_it3.497
r_scbond_it2.415
r_angle_refined_deg1.663
r_mcangle_it1.637
r_mcbond_it1.108
r_nbtor_refined0.313
r_nbd_refined0.2
r_symmetry_vdw_refined0.182
r_xyhbond_nbd_refined0.146
r_chiral_restr0.113
r_symmetry_hbond_refined0.071
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1518
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms54

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling