2FGV

X-ray crystal structure of HIV-1 Protease T80N 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
2.0941.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.52α = 90
b = 58.18β = 90
c = 61.52γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVOsmic Mirrors2004-11-04MSINGLE 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
11.542.2699.30.0420.04217.74.22964729647

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 1F7A1.542.262964728102149999.380.17260.172650.171380.19722RANDOM16.077
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]
-0.330.170.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.026
r_dihedral_angle_4_deg15.07
r_dihedral_angle_3_deg10.54
r_dihedral_angle_1_deg6.181
r_scangle_it2.119
r_scbond_it1.429
r_angle_refined_deg1.376
r_mcangle_it0.873
r_mcbond_it0.724
r_angle_other_deg0.717
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.026
r_dihedral_angle_4_deg15.07
r_dihedral_angle_3_deg10.54
r_dihedral_angle_1_deg6.181
r_scangle_it2.119
r_scbond_it1.429
r_angle_refined_deg1.376
r_mcangle_it0.873
r_mcbond_it0.724
r_angle_other_deg0.717
r_symmetry_hbond_refined0.189
r_nbd_refined0.186
r_symmetry_vdw_other0.177
r_nbd_other0.174
r_nbtor_refined0.17
r_mcbond_other0.164
r_xyhbond_nbd_refined0.159
r_symmetry_vdw_refined0.113
r_chiral_restr0.085
r_nbtor_other0.08
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1494
Nucleic Acid Atoms
Solvent Atoms193
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing