3KFR

HIV Protease (PR) dimer with inhibitor TL-3 bound and fragment 1F1 in the outside/top of flap


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AZ8HIV PR dimer generated from monomer with TL-3 bound in 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
2.0138.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 28.72α = 90
b = 65.57β = 90
c = 92.36γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rRh coated flat mirror2008-12-08MSINGLE 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
11.1525.397.80.0510.0516.73.8630486166112
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)
11.151.1896.60.80.80.93.94432

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 monomer with TL-3 bound in 2AZ81.325.3429722151980.1840.1830.207RANDOM16.693
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]
0.09-0.02-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.783
r_dihedral_angle_4_deg13.812
r_dihedral_angle_3_deg10.527
r_dihedral_angle_1_deg6.481
r_sphericity_free4.003
r_scangle_it3.801
r_sphericity_bonded3.197
r_scbond_it2.434
r_mcangle_it1.928
r_angle_refined_deg1.437
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.783
r_dihedral_angle_4_deg13.812
r_dihedral_angle_3_deg10.527
r_dihedral_angle_1_deg6.481
r_sphericity_free4.003
r_scangle_it3.801
r_sphericity_bonded3.197
r_scbond_it2.434
r_mcangle_it1.928
r_angle_refined_deg1.437
r_rigid_bond_restr1.29
r_mcbond_it1.182
r_chiral_restr0.086
r_bond_refined_d0.01
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1520
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms86

Software

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