3KFN

HIV Protease (PR) with inhibitor TL-3 and fragment hit 4D9 by soaking


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION72770.5 M KSCN, 0.1 M MES-HCL, pH 7.0, 10% DMSO, VAPOR DIFFUSION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7154.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.95α = 90
b = 85.57β = 90
c = 46.49γ = 90
Symmetry
Space GroupP 21 21 2

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
11.7748.56493.70.0890.08933.4233682189627.9
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)
11.771.8292.50.6370.6371.13.41574

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 PR dimer generated from PDB entry 2AZ81.7748.552336821866113692.580.2170.2140.274RANDOM32.903
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]
3.68-1.94-1.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.718
r_dihedral_angle_4_deg20.329
r_dihedral_angle_3_deg14.318
r_dihedral_angle_1_deg6.461
r_scangle_it4.955
r_scbond_it3.357
r_mcangle_it2.217
r_angle_refined_deg1.884
r_mcbond_it1.346
r_chiral_restr0.145
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.718
r_dihedral_angle_4_deg20.329
r_dihedral_angle_3_deg14.318
r_dihedral_angle_1_deg6.461
r_scangle_it4.955
r_scbond_it3.357
r_mcangle_it2.217
r_angle_refined_deg1.884
r_mcbond_it1.346
r_chiral_restr0.145
r_bond_refined_d0.023
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1518
Nucleic Acid Atoms
Solvent Atoms201
Heterogen Atoms96

Software

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