6OGT

X-ray crystal structure of darunavir-resistant HIV-1 protease (P51) in complex with GRL-001


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5TYR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.22980.15 M (NH4)2SO4, 0.1 M HEPES (pH 7.2), 20% (v/v) PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.1743.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.071α = 90
b = 63.071β = 90
c = 82.196γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-07-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.2154.6296.322.3214.328980
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.211.25

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT5TYR1.2154.6227537139396.140.192650.1920.206RANDOM16.02
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]
0.160.080.16-0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.795
r_dihedral_angle_3_deg9.806
r_dihedral_angle_1_deg7.801
r_long_range_B_other5.337
r_long_range_B_refined5.334
r_scangle_other4.065
r_dihedral_angle_4_deg3.851
r_scbond_it2.612
r_scbond_other2.612
r_mcangle_other2.462
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.795
r_dihedral_angle_3_deg9.806
r_dihedral_angle_1_deg7.801
r_long_range_B_other5.337
r_long_range_B_refined5.334
r_scangle_other4.065
r_dihedral_angle_4_deg3.851
r_scbond_it2.612
r_scbond_other2.612
r_mcangle_other2.462
r_mcangle_it2.46
r_angle_refined_deg2.124
r_angle_other_deg1.995
r_mcbond_it1.598
r_mcbond_other1.586
r_chiral_restr0.124
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_bond_other_d0.009
r_gen_planes_other0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms764
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing