2Z4O

Wild Type HIV-1 Protease with potent Antiviral inhibitor GRL-98065


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FG6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.829825mM sodium acetate, 10% (w/v) sodium chloride, 6% dioxane, 10% (v/v) dimethylsulfoxide (DMSO), pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6753.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.25α = 90
b = 85.832β = 90
c = 45.967γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4doubly focusing toroidal mirror2002-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X26C0.9561NSLSX26C

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
11.65099.70.071115.2311283102015.3
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)
1.61.6699.40.3884.75.23029

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1FG61.6103087530846155399.70.14720.14380.2055RANDOM
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
2216311761.28
RMS Deviations
KeyRefinement Restraint Deviation
s_approx_iso_adps0.079
s_similar_adp_cmpnt0.033
s_angle_d0.029
s_from_restr_planes0.0274
s_non_zero_chiral_vol0.025
s_zero_chiral_vol0.014
s_anti_bump_dis_restr0.011
s_bond_d0.009
s_rigid_bond_adp_cmpnt0.002
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1605
Nucleic Acid Atoms
Solvent Atoms238
Heterogen Atoms87

Software

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