6OYR

X-ray crystal structure of wild type HIV-1 protease in complex with GRL-002


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42980.15 M Ammonium sulfate, 0.1 M HEPES (pH 7.4), 15% (w/v) PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.1743.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.82α = 90
b = 62.82β = 90
c = 82.354γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-10-31MSINGLE 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
11.5445.3999.3215.7218.614722
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.541.595

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 REPLACEMENTTHROUGHOUT5TYR1.5445.391397673799.350.217840.215560.26119RANDOM24.835
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]
0.150.070.15-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.39
r_dihedral_angle_4_deg16.844
r_dihedral_angle_3_deg11.077
r_dihedral_angle_1_deg8.304
r_long_range_B_refined5.636
r_long_range_B_other5.633
r_scangle_other4.209
r_mcangle_other2.956
r_mcangle_it2.955
r_scbond_it2.822
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.39
r_dihedral_angle_4_deg16.844
r_dihedral_angle_3_deg11.077
r_dihedral_angle_1_deg8.304
r_long_range_B_refined5.636
r_long_range_B_other5.633
r_scangle_other4.209
r_mcangle_other2.956
r_mcangle_it2.955
r_scbond_it2.822
r_scbond_other2.819
r_mcbond_it2.122
r_mcbond_other2.113
r_angle_refined_deg2.033
r_angle_other_deg1.957
r_chiral_restr0.105
r_bond_refined_d0.022
r_gen_planes_refined0.014
r_gen_planes_other0.009
r_bond_other_d0.008
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 Atoms760
Nucleic Acid Atoms
Solvent Atoms43
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
xia2data scaling
MOLREPphasing