3KFS

HIV Protease (PR) dimer with inhibitor TL-3 bound and fragment 2F4 in the outside/top of flap


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AZ8HIV Protease dimer generated from PDB entry 2AZ8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.82770.5 M KSCN, 0.1 M MES-HCL, pH 5.8, 10% DMSO, VAPOR DIFFUSION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0640.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 28.95α = 90
b = 66.35β = 90
c = 92.97γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rRh coated flat mirror2009-04-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-10.97946SSRLBL7-1

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
11.846.599.50.1380.1383.93.8173331724616.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8598.80.7150.7151.13.91225

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTHIV Protease dimer generated from PDB entry 2AZ81.838.07173331719987299.390.2050.2030.25RANDOM19.249
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]
-0.361.45-1.09
RMS Deviations
KeyRefinement Restraint Deviation
r_angle_refined_deg2.11
r_bond_refined_d0.024
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1518
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms99

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing