2FGU

X-ray crystal structure of HIV-1 Protease T80S variant in complex with the inhibitor saquinavir used to explore the role of invariant Thr80 in HIV-1 protease structure, function, and viral infectivity.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1F7Apdb entry 1F7A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52980.126 M Sodium Phosphate pH 6.2, 0.063 M Sodium Citrate, 23-24% Ammonium Sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0941.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.5α = 90
b = 57.93β = 90
c = 61.62γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVOsmic Mirrors2004-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
1242.2299.10.0730.0738.271262512625

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1F7A242.22126251197761299.090.17910.179110.17640.23235RANDOM21.948
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]
-0.730.520.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.207
r_dihedral_angle_4_deg27.859
r_dihedral_angle_3_deg12.644
r_dihedral_angle_1_deg6.942
r_scangle_it3.321
r_scbond_it2.217
r_angle_refined_deg1.613
r_mcangle_it1.443
r_mcbond_it1.2
r_angle_other_deg0.679
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.207
r_dihedral_angle_4_deg27.859
r_dihedral_angle_3_deg12.644
r_dihedral_angle_1_deg6.942
r_scangle_it3.321
r_scbond_it2.217
r_angle_refined_deg1.613
r_mcangle_it1.443
r_mcbond_it1.2
r_angle_other_deg0.679
r_mcbond_other0.263
r_symmetry_hbond_refined0.216
r_nbd_other0.213
r_nbd_refined0.199
r_xyhbond_nbd_refined0.19
r_symmetry_vdw_other0.177
r_nbtor_refined0.176
r_chiral_restr0.093
r_nbtor_other0.092
r_xyhbond_nbd_other0.073
r_symmetry_vdw_refined0.062
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_gen_planes_other0.001
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1462
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing