3EKT

Crystal Structure of the inhibitor Darunavir (DRV) in complex with a multi-drug resistant HIV-1 protease variant (L10F/G48V/I54V/V64I/V82A) (Refer: FLAP+ in citation.)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2298Refer citation, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
358.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.013α = 90
b = 92.013β = 90
c = 106.161γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray133IMAGE PLATERIGAKU RAXIS IVMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.974095.80.0515.43457834578

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 REPLACEMENTTHROUGHOUT1.974034447171395.590.2110.2090.258RANDOM13.827
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]
0.390.190.39-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.761
r_dihedral_angle_4_deg15.716
r_dihedral_angle_3_deg13.938
r_dihedral_angle_1_deg6.67
r_scangle_it2.424
r_scbond_it1.711
r_angle_refined_deg1.12
r_angle_other_deg1.06
r_mcangle_it0.987
r_mcbond_it0.897
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.761
r_dihedral_angle_4_deg15.716
r_dihedral_angle_3_deg13.938
r_dihedral_angle_1_deg6.67
r_scangle_it2.424
r_scbond_it1.711
r_angle_refined_deg1.12
r_angle_other_deg1.06
r_mcangle_it0.987
r_mcbond_it0.897
r_symmetry_hbond_refined0.255
r_nbd_other0.224
r_xyhbond_nbd_refined0.217
r_symmetry_vdw_refined0.203
r_symmetry_vdw_other0.2
r_nbd_refined0.195
r_xyhbond_nbd_other0.182
r_nbtor_refined0.181
r_mcbond_other0.116
r_nbtor_other0.087
r_chiral_restr0.074
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2948
Nucleic Acid Atoms
Solvent Atoms321
Heterogen Atoms133

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction