2P3B

Crystal Structure of the subtype B wild type HIV protease complexed with TL-3 inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherCrystal Structure of the multi-drug resistant mutant subtype B HIV protease complexed with TL-3 inhibitor

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.227715% saturated ammonium sulfate solution, 6% (v/v) MPD, 85mM sodium citrate/170mM sodium phosphate, 0.02% sodium azide, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2144.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.164α = 90
b = 63.164β = 90
c = 83.414γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATEMAR scanner 345 mm plateMIRRORS1998-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
12.154.7299.70.07513.63.711047
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)
12.12.211000.4142.73.71587

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 REPLACEMENTTHROUGHOUTCrystal Structure of the multi-drug resistant mutant subtype B HIV protease complexed with TL-3 inhibitor2.116.5811011108499.820.1650.1590.219RANDOM31.322
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]
0.040.020.04-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.853
r_dihedral_angle_4_deg18.41
r_dihedral_angle_3_deg17.262
r_sphericity_bonded13.27
r_dihedral_angle_1_deg6.534
r_scangle_it3.911
r_mcangle_it2.84
r_scbond_it2.785
r_rigid_bond_restr1.947
r_mcbond_it1.638
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.853
r_dihedral_angle_4_deg18.41
r_dihedral_angle_3_deg17.262
r_sphericity_bonded13.27
r_dihedral_angle_1_deg6.534
r_scangle_it3.911
r_mcangle_it2.84
r_scbond_it2.785
r_rigid_bond_restr1.947
r_mcbond_it1.638
r_angle_refined_deg1.575
r_nbtor_refined0.32
r_xyhbond_nbd_refined0.23
r_nbd_refined0.222
r_symmetry_vdw_refined0.172
r_symmetry_hbond_refined0.111
r_chiral_restr0.085
r_bond_refined_d0.015
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1520
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms66

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
PHASERphasing