8FUJ

HIV-1 wild type protease with GRL-03419A, with N-(2,5-dimethylphenyl)-4-(pyridin-3-yl)pyrimidin-2-amine as P2-P3 group and 3,5-difluorophenylmethyl as the P1 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 DROP62980.57M sodium chloride and 0.1 M sodium acetate, pH 6.0
Crystal Properties
Matthews coefficientSolvent content
2.754.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.609α = 90
b = 86.214β = 90
c = 46.189γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-06-05MSINGLE 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
11.125093.40.06816.95.5844946.894
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)
11.121.1656.10.3371.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.1236.380315412493.350.121350.12060.13584RANDOM10.509
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]
0.33-0.21-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.346
r_dihedral_angle_1_deg6.914
r_rigid_bond_restr5.643
r_dihedral_angle_2_deg4.265
r_scangle_other3.276
r_long_range_B_refined3.149
r_long_range_B_other3.004
r_scbond_it2.905
r_scbond_other2.901
r_angle_refined_deg1.943
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.346
r_dihedral_angle_1_deg6.914
r_rigid_bond_restr5.643
r_dihedral_angle_2_deg4.265
r_scangle_other3.276
r_long_range_B_refined3.149
r_long_range_B_other3.004
r_scbond_it2.905
r_scbond_other2.901
r_angle_refined_deg1.943
r_mcangle_it1.72
r_mcangle_other1.72
r_mcbond_it1.307
r_mcbond_other1.307
r_angle_other_deg0.782
r_chiral_restr0.128
r_gen_planes_other0.016
r_bond_refined_d0.014
r_gen_planes_refined0.014
r_bond_other_d0.004
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 Atoms312
Heterogen Atoms69

Software

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