7TO5

HIV-1 wild type protease with GRL-05816A, with C-4 substituted cyclohexane-fused bis-tetrahydrofuran (Chf-THF) derivatives as P2-ligand [diastereomer 1]


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NU3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62980.5 M NaCl, 0.1M Sodium Acetate, pH 6.0
Crystal Properties
Matthews coefficientSolvent content
2.7254.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.943α = 90
b = 86.138β = 90
c = 46.097γ = 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)Rrim I (All)Rpim I (All)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
11.135091.60.060.0630.01824.58.880849
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.131.1752.10.410.4820.2480.8683.4

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 REPLACEMENTTHROUGHOUT3NU31.1336.3476823397691.480.12360.12260.1422RANDOM12.164
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]
0.44-0.26-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.199
r_dihedral_angle_4_deg14.643
r_dihedral_angle_3_deg10.995
r_dihedral_angle_1_deg6.723
r_rigid_bond_restr4.866
r_angle_refined_deg2.701
r_angle_other_deg1.524
r_chiral_restr0.907
r_bond_refined_d0.023
r_gen_planes_refined0.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.199
r_dihedral_angle_4_deg14.643
r_dihedral_angle_3_deg10.995
r_dihedral_angle_1_deg6.723
r_rigid_bond_restr4.866
r_angle_refined_deg2.701
r_angle_other_deg1.524
r_chiral_restr0.907
r_bond_refined_d0.023
r_gen_planes_refined0.014
r_gen_planes_other0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1512
Nucleic Acid Atoms
Solvent Atoms279
Heterogen Atoms111

Software

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