2Q5K

Crystal structure of lopinavir bound to wild type HIV-1 protease


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1F7Apdb entry 1F7A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2298126mM sodium phosphate, 63mM sodium citrate, 24-29% ammonium sulphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.141.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.343α = 90
b = 58.043β = 90
c = 61.133γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATERIGAKU RAXIS IVosmic mirrors2005-03-18MSINGLE 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
11.9550970.0444.419.63.413461

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 REPLACEMENTTHROUGHOUTpdb entry 1F7A1.9542.111275267597.060.194210.191960.236RANDOM34.254
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]
-0.90.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.51
r_dihedral_angle_4_deg21.021
r_dihedral_angle_3_deg11.925
r_dihedral_angle_1_deg5.992
r_scangle_it1.586
r_angle_refined_deg1.195
r_scbond_it1.03
r_angle_other_deg0.725
r_mcangle_it0.583
r_mcbond_it0.407
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.51
r_dihedral_angle_4_deg21.021
r_dihedral_angle_3_deg11.925
r_dihedral_angle_1_deg5.992
r_scangle_it1.586
r_angle_refined_deg1.195
r_scbond_it1.03
r_angle_other_deg0.725
r_mcangle_it0.583
r_mcbond_it0.407
r_nbd_refined0.177
r_nbd_other0.175
r_nbtor_refined0.165
r_symmetry_hbond_refined0.152
r_symmetry_vdw_other0.143
r_xyhbond_nbd_refined0.141
r_xyhbond_nbd_other0.108
r_symmetry_vdw_refined0.099
r_mcbond_other0.095
r_nbtor_other0.078
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms1485
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms66

Software

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