5T2Z

Crystal Structure of Multi-drug Resistant HIV-1 Protease PR-S17 in Complex with Darunavir


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UCB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729835% Tacsimate, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.1943.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.851α = 90
b = 62.851β = 90
c = 82.961γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMIRRORS2015-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1APS22-ID

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
11.55098.90.05724.85.729451
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5597.80.4090.8984.25

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 REPLACEMENTTHROUGHOUT3UCB1.532.9927947148698.970.145360.142360.19547RANDOM34.91
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]
0.080.040.08-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.963
r_sphericity_free24.911
r_dihedral_angle_4_deg18.001
r_sphericity_bonded16.549
r_dihedral_angle_3_deg14.714
r_dihedral_angle_1_deg8.053
r_long_range_B_refined7.162
r_long_range_B_other7.037
r_scangle_other6.912
r_scbond_it6.378
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.963
r_sphericity_free24.911
r_dihedral_angle_4_deg18.001
r_sphericity_bonded16.549
r_dihedral_angle_3_deg14.714
r_dihedral_angle_1_deg8.053
r_long_range_B_refined7.162
r_long_range_B_other7.037
r_scangle_other6.912
r_scbond_it6.378
r_scbond_other6.375
r_rigid_bond_restr6.339
r_mcangle_other5.576
r_mcangle_it5.565
r_mcbond_it5.07
r_mcbond_other5.04
r_angle_refined_deg2.749
r_angle_other_deg1.624
r_chiral_restr0.176
r_bond_refined_d0.031
r_gen_planes_refined0.013
r_gen_planes_other0.008
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1522
Nucleic Acid Atoms
Solvent Atoms90
Heterogen Atoms38

Software

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