6OGQ

X-ray crystal structure of darunavir-resistant HIV-1 protease (P30) in complex with GRL-003


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72980.15 M Ammonium sulfate, 0.1 M HEPES (pH 7.0), 25% (w/v) PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.1743.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.823α = 90
b = 62.823β = 90
c = 82.154γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-11-01MSINGLE 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
11.4145.3699.9112.7518.219097
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.411.46

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 REPLACEMENTTHROUGHOUT5TYR1.4145.361812995999.940.200360.198530.23452RANDOM18.635
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]
0.260.130.26-0.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.965
r_dihedral_angle_3_deg12.282
r_dihedral_angle_4_deg10.133
r_dihedral_angle_1_deg7.144
r_long_range_B_other5.327
r_long_range_B_refined5.324
r_scangle_other3.915
r_scbond_it2.893
r_scbond_other2.562
r_mcangle_other2.245
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.965
r_dihedral_angle_3_deg12.282
r_dihedral_angle_4_deg10.133
r_dihedral_angle_1_deg7.144
r_long_range_B_other5.327
r_long_range_B_refined5.324
r_scangle_other3.915
r_scbond_it2.893
r_scbond_other2.562
r_mcangle_other2.245
r_mcangle_it2.243
r_angle_refined_deg1.834
r_angle_other_deg1.592
r_mcbond_it1.55
r_mcbond_other1.539
r_chiral_restr0.081
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.004
r_gen_planes_other0.002
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 Atoms758
Nucleic Acid Atoms
Solvent Atoms42
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing