6OYD

X-ray crystal structure of wild type HIV-1 protease in complex with GRL-004


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52980.2 M Sodium chloride, 0.1 M MES (pH 6.5), 10%(w/v) PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.1643.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.825α = 90
b = 62.825β = 90
c = 82.28γ = 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
11.4654.4199.6314.118.617208
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.461.512

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 REPLACEMENTTHROUGHOUT5TYR1.4654.411634586099.640.220090.218190.25721RANDOM23.611
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]
0.050.020.05-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.707
r_dihedral_angle_4_deg24.206
r_dihedral_angle_3_deg13.384
r_dihedral_angle_1_deg8.104
r_long_range_B_other5.926
r_long_range_B_refined5.923
r_scangle_other4.723
r_scbond_it3.136
r_scbond_other3.132
r_mcangle_it3.091
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.707
r_dihedral_angle_4_deg24.206
r_dihedral_angle_3_deg13.384
r_dihedral_angle_1_deg8.104
r_long_range_B_other5.926
r_long_range_B_refined5.923
r_scangle_other4.723
r_scbond_it3.136
r_scbond_other3.132
r_mcangle_it3.091
r_mcangle_other3.091
r_mcbond_it2.294
r_mcbond_other2.289
r_angle_refined_deg2.003
r_angle_other_deg1.62
r_chiral_restr0.095
r_bond_refined_d0.015
r_gen_planes_refined0.015
r_gen_planes_other0.009
r_bond_other_d0.003
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 Atoms760
Nucleic Acid Atoms
Solvent Atoms31
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing