3EKX

Crystal structure of the wild-type HIV-1 protease with the inhibitor, Nelfinavir


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1F7A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2300126mM Sodium Phosphate pH 6.2; 63mM sodium citrate; 24-29% ammonium sulphate , VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.141.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.924α = 90
b = 57.848β = 90
c = 61.572γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATERIGAKU RAXIS IVYale mirrorsMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.975098.40.0490.04922.66.113251

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1F7A1.9739.251255765298.330.1840.186270.1840.22999RANDOM33.032
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]
-1.121.63-0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.068
r_dihedral_angle_3_deg13.841
r_dihedral_angle_4_deg10.493
r_dihedral_angle_1_deg6.147
r_scangle_it1.868
r_angle_other_deg1.641
r_angle_refined_deg1.327
r_scbond_it1.224
r_mcangle_it0.791
r_mcbond_it0.657
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.068
r_dihedral_angle_3_deg13.841
r_dihedral_angle_4_deg10.493
r_dihedral_angle_1_deg6.147
r_scangle_it1.868
r_angle_other_deg1.641
r_angle_refined_deg1.327
r_scbond_it1.224
r_mcangle_it0.791
r_mcbond_it0.657
r_symmetry_hbond_refined0.4
r_nbd_other0.198
r_symmetry_vdw_other0.187
r_nbd_refined0.184
r_nbtor_refined0.168
r_xyhbond_nbd_refined0.164
r_mcbond_other0.123
r_symmetry_vdw_refined0.092
r_nbtor_other0.085
r_chiral_restr0.072
r_gen_planes_other0.018
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1490
Nucleic Acid Atoms
Solvent Atoms118
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing