3LZU

Crystal Structure of a Nelfinavir Resistant HIV-1 CRF01_AE Protease variant (N88S) in Complex with the Protease Inhibitor Darunavir.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TSU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2295126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 18-33% Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.1141.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.878α = 90
b = 61.878β = 90
c = 82.15γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315bent conical Si, Rh coating2008-11-07SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.90APS14-BM-C

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
11.7653.6197.40.04119.64.679445
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)
1.761.8279.40.4012.61408

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1TSU1.7653.6179445872980.1980.1960.239RANDOM33.054
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]
0.340.170.34-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.829
r_dihedral_angle_4_deg13.27
r_dihedral_angle_3_deg12.438
r_dihedral_angle_1_deg8.2
r_scangle_it2.909
r_scbond_it2.227
r_angle_refined_deg1.7
r_mcangle_it1.403
r_mcbond_it1.207
r_angle_other_deg0.899
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.829
r_dihedral_angle_4_deg13.27
r_dihedral_angle_3_deg12.438
r_dihedral_angle_1_deg8.2
r_scangle_it2.909
r_scbond_it2.227
r_angle_refined_deg1.7
r_mcangle_it1.403
r_mcbond_it1.207
r_angle_other_deg0.899
r_mcbond_other0.253
r_nbd_refined0.21
r_nbd_other0.206
r_symmetry_vdw_other0.188
r_nbtor_refined0.176
r_symmetry_vdw_refined0.171
r_xyhbond_nbd_refined0.156
r_symmetry_hbond_refined0.105
r_chiral_restr0.098
r_nbtor_other0.088
r_xyhbond_nbd_other0.017
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1463
Nucleic Acid Atoms
Solvent Atoms81
Heterogen Atoms58

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
BioCARSdata collection
HKL-2000data reduction