4LL3

Structure of wild-type HIV protease in complex with darunavir


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1RESERVOIR: 2 M SODIUM FORMATE, 0.1 M SODIUM ACETATE, PH 4.6. DROPS: 2 UL PROTEIN + 1UL RESERVOIR, PROTEIN CONCENTRATION 5MG/ML, 5-FOLD MOLAR EXCESS OF INHIBITOR (DISSOLVED IN DMSO) OVER PROTEIN, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K
Crystal Properties
Matthews coefficientSolvent content
2.1241.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.557α = 90
b = 62.557β = 90
c = 81.523γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-05-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X12EMBL/DESY, HAMBURGX12

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
11.955099.90.0626.456.713257
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)
11.952.0299.90.5132.75.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.9527.091255866299.950.185230.182880.23RANDOM36.773
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]
-0.23-0.11-0.230.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.981
r_dihedral_angle_4_deg18.813
r_dihedral_angle_3_deg14.079
r_dihedral_angle_1_deg6.332
r_scangle_it3.084
r_scbond_it1.908
r_angle_refined_deg1.508
r_mcangle_it1.301
r_mcbond_it1.296
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.981
r_dihedral_angle_4_deg18.813
r_dihedral_angle_3_deg14.079
r_dihedral_angle_1_deg6.332
r_scangle_it3.084
r_scbond_it1.908
r_angle_refined_deg1.508
r_mcangle_it1.301
r_mcbond_it1.296
r_nbtor_refined0.314
r_symmetry_vdw_refined0.233
r_nbd_refined0.209
r_xyhbond_nbd_refined0.171
r_symmetry_hbond_refined0.134
r_chiral_restr0.1
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1520
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms76

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling