2P3C

Crystal Structure of the subtype F 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 DROP6.22910.8M ammonium sulfate, 0.1M sodium cacodylate. The crystals nucleated at 277K and were transfered to 291K for further growth. The protein to well proportion was 2:1, pH 6.2, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.0539.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.425α = 90
b = 61.425β = 90
c = 80.892γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMSINGLE WAVELENGTH
21x-rayM
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE D03B-MX1LNLSD03B-MX1

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
1,22.153.22599.70.0460.04610.82.510162
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)
1,22.12.2199.80.3180.3182.12.41491

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 inhibitor2.125.2710121100899.670.2010.1940.265RANDOM35.515
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]
-0.01-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.814
r_dihedral_angle_4_deg25.096
r_dihedral_angle_3_deg18.909
r_sphericity_bonded14.499
r_dihedral_angle_1_deg7.07
r_scangle_it3.333
r_mcangle_it2.749
r_scbond_it2.391
r_rigid_bond_restr1.689
r_angle_refined_deg1.593
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.814
r_dihedral_angle_4_deg25.096
r_dihedral_angle_3_deg18.909
r_sphericity_bonded14.499
r_dihedral_angle_1_deg7.07
r_scangle_it3.333
r_mcangle_it2.749
r_scbond_it2.391
r_rigid_bond_restr1.689
r_angle_refined_deg1.593
r_mcbond_it1.546
r_nbtor_refined0.322
r_symmetry_vdw_refined0.243
r_nbd_refined0.231
r_xyhbond_nbd_refined0.201
r_symmetry_hbond_refined0.131
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1504
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms78

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
CCP4data scaling
PHASERphasing