6OGP

X-ray crystal structure of wild type HIV-1 protease in complex with GRL-063


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), 20% (w/v) PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.1843.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.087α = 90
b = 63.087β = 90
c = 82.339γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-12-02MSINGLE 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
11.5354.6310015.3318.515238
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.531.58

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 REPLACEMENTTHROUGHOUT5TYR1.531.581444175999.960.220780.21860.2623RANDOM24.97
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]
0.220.110.22-0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.435
r_dihedral_angle_4_deg12.954
r_dihedral_angle_3_deg10.742
r_dihedral_angle_1_deg8.106
r_long_range_B_refined5.239
r_long_range_B_other5.237
r_scangle_other4.126
r_mcangle_it2.794
r_mcangle_other2.794
r_scbond_it2.741
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.435
r_dihedral_angle_4_deg12.954
r_dihedral_angle_3_deg10.742
r_dihedral_angle_1_deg8.106
r_long_range_B_refined5.239
r_long_range_B_other5.237
r_scangle_other4.126
r_mcangle_it2.794
r_mcangle_other2.794
r_scbond_it2.741
r_scbond_other2.738
r_angle_refined_deg2.072
r_mcbond_it1.997
r_mcbond_other1.99
r_angle_other_deg1.951
r_chiral_restr0.113
r_bond_refined_d0.024
r_gen_planes_refined0.014
r_gen_planes_other0.009
r_bond_other_d0.007
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 Atoms34
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing