3EKV

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1F7APDB ENTRY 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
2.0840.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.723α = 90
b = 57.401β = 90
c = 61.741γ = 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
11.755079.70.0290.029193.314987

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1F7A1.7539.191421375679.780.190.190.189790.2261RANDOM20.564
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]
-1.672.02-0.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.17
r_dihedral_angle_4_deg18.365
r_dihedral_angle_3_deg13.624
r_dihedral_angle_1_deg6.682
r_scangle_it2.186
r_scbond_it1.568
r_angle_refined_deg1.414
r_mcangle_it0.917
r_mcbond_it0.775
r_angle_other_deg0.753
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.17
r_dihedral_angle_4_deg18.365
r_dihedral_angle_3_deg13.624
r_dihedral_angle_1_deg6.682
r_scangle_it2.186
r_scbond_it1.568
r_angle_refined_deg1.414
r_mcangle_it0.917
r_mcbond_it0.775
r_angle_other_deg0.753
r_symmetry_hbond_refined0.297
r_nbd_refined0.184
r_nbd_other0.182
r_mcbond_other0.18
r_nbtor_refined0.167
r_symmetry_vdw_other0.163
r_xyhbond_nbd_refined0.136
r_symmetry_vdw_refined0.129
r_chiral_restr0.086
r_nbtor_other0.083
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1490
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms51

Software

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