8FUI

HIV-1 wild type protease with GRL-02519A, with N-(2,5-dimethylphenyl)-4-(pyridin-3-yl)pyrimidin-2-amine as P2-P3 group


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NU3HIV-1 wild type protease with Amprenavir

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.42981.1 M NaCl, 0.1 M Sodium Acetate, pH 5.4
Crystal Properties
Matthews coefficientSolvent content
2.754.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.451α = 90
b = 86.136β = 90
c = 46.113γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.255092.10.10411.85.56003613.999
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.251.2950.10.3831.7

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 REPLACEMENTTHROUGHOUT3NU31.2533.456906307992.090.140830.138980.17555RANDOM16.194
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]
-0.49-1.081.57
RMS Deviations
KeyRefinement Restraint Deviation
r_rigid_bond_restr18.096
r_dihedral_angle_3_deg12.55
r_dihedral_angle_1_deg7.019
r_long_range_B_other6.506
r_long_range_B_refined6.505
r_scangle_other5.998
r_scbond_other5.973
r_scbond_it5.967
r_dihedral_angle_2_deg5.363
r_mcangle_it3.108
RMS Deviations
KeyRefinement Restraint Deviation
r_rigid_bond_restr18.096
r_dihedral_angle_3_deg12.55
r_dihedral_angle_1_deg7.019
r_long_range_B_other6.506
r_long_range_B_refined6.505
r_scangle_other5.998
r_scbond_other5.973
r_scbond_it5.967
r_dihedral_angle_2_deg5.363
r_mcangle_it3.108
r_mcangle_other3.108
r_mcbond_it2.436
r_mcbond_other2.435
r_angle_refined_deg1.764
r_angle_other_deg0.671
r_chiral_restr0.112
r_gen_planes_other0.019
r_gen_planes_refined0.013
r_bond_refined_d0.012
r_bond_other_d0.007
r_dihedral_angle_4_deg
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1512
Nucleic Acid Atoms
Solvent Atoms250
Heterogen Atoms71

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction