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 Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 298.0
Details 0.126 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 Data

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

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV Osmic Mirrors 2004-11-05
Diffraction Radiation
Monochromator Protocol
Osmic Mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2 42.22 99.1 0.073 0.073 -- 7.0 12625 12625 0.0 0.0 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.0 42.22 0.0 0.0 12625 11977 612 99.09 0.1791 0.17911 0.1764 0.23235 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.0 2.052 -- 47 783 0.235 0.331 -- 90.91
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 21.948
Anisotropic B[1][1] -0.73
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.52
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.21
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_other 0.177
r_xyhbond_nbd_refined 0.19
r_xyhbond_nbd_other 0.073
r_angle_refined_deg 1.613
r_scangle_it 3.321
r_bond_other_d 0.0
r_nbtor_refined 0.176
r_dihedral_angle_4_deg 27.859
r_nbtor_other 0.092
r_angle_other_deg 0.679
r_nbd_other 0.213
r_gen_planes_other 0.001
r_symmetry_hbond_refined 0.216
r_chiral_restr 0.093
r_gen_planes_refined 0.004
r_dihedral_angle_1_deg 6.942
r_symmetry_vdw_refined 0.062
r_dihedral_angle_2_deg 42.207
r_mcbond_other 0.263
r_scbond_it 2.217
r_dihedral_angle_3_deg 12.644
r_mcangle_it 1.443
r_nbd_refined 0.199
r_mcbond_it 1.2
r_bond_refined_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1462
Nucleic Acid Atoms 0
Heterogen Atoms 74
Solvent Atoms 130

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
SCALEPACK data scaling
AMoRE phasing