3EKQ

Crystal structure of inhibitor saquinavir (SQV) in complex with multi-drug resistant HIV-1 protease (L63P/V82T/I84V) (referred to as ACT in paper)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1F7APDB ENTRY 1F7A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2300pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.1542.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.164α = 90
b = 59.291β = 90
c = 61.389γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray300IMAGE PLATERIGAKU RAXIS IVYale Mirrors2008-01-28MSINGLE 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
124297.20.070.0766.61297512975

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 DIFFRACTIONTHROUGHOUTPDB ENTRY 1F7A2.220975146798.380.1970.1950.246RANDOM34.606
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]
-1.14-1.192.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.441
r_dihedral_angle_4_deg14.06
r_dihedral_angle_3_deg13.593
r_dihedral_angle_1_deg6.953
r_scangle_it2.212
r_scbond_it1.66
r_angle_refined_deg1.273
r_mcbond_it1.063
r_mcangle_it1.022
r_angle_other_deg0.714
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.441
r_dihedral_angle_4_deg14.06
r_dihedral_angle_3_deg13.593
r_dihedral_angle_1_deg6.953
r_scangle_it2.212
r_scbond_it1.66
r_angle_refined_deg1.273
r_mcbond_it1.063
r_mcangle_it1.022
r_angle_other_deg0.714
r_nbd_other0.205
r_nbd_refined0.179
r_nbtor_refined0.169
r_symmetry_vdw_refined0.167
r_xyhbond_nbd_refined0.158
r_symmetry_vdw_other0.147
r_mcbond_other0.124
r_nbtor_other0.087
r_chiral_restr0.077
r_symmetry_hbond_refined0.072
r_xyhbond_nbd_other0.032
r_bond_refined_d0.008
r_bond_other_d0.005
r_gen_planes_refined0.004
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1477
Nucleic Acid Atoms
Solvent Atoms74
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing