3NU6

Crystal Structure of HIV-1 Protease Mutant I54M with Antiviral Drug Amprenavir


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2F8G 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6298Crystal was grown by the hanging-drop vapor-diffusion method at room temperature, from a 2.2 mg/ml protein solution at pH 4.6 with 0.1M sodium acetate, 0.67M sodium chloride. The inhibitor was mixed with protease in a ratio 5:1 , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6754.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.12α = 90
b = 85.91β = 90
c = 46.1γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2007-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-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
11.165091.80.072510.6
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)
1.161.258.90.35722.1

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 DIFFRACTIONAB INITIOFREE R2F8G1.16107346373463368091.60.15420.15230.15230.1879RANDOM
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
111648.371765.77
RMS Deviations
KeyRefinement Restraint Deviation
s_approx_iso_adps0.101
s_anti_bump_dis_restr0.089
s_non_zero_chiral_vol0.077
s_zero_chiral_vol0.072
s_similar_adp_cmpnt0.04
s_angle_d0.033
s_from_restr_planes0.0289
s_bond_d0.016
s_rigid_bond_adp_cmpnt0.005
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1512
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms47

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling