5T2E

Crystal Structure of multi-drug resistant HIV-1 protease PR-S17


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UF3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.62982.1M sodium chloride and 0.1M HEPES pH7.6
Crystal Properties
Matthews coefficientSolvent content
2.8857.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.899α = 90
b = 49.899β = 90
c = 86.628γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMirrors2015-10-26MSINGLE 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
11.55099.50.05725.225.620429
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)
11.51.5599.50.4470.8493.093.8

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 REPLACEMENTTHROUGHOUT3UF31.530.5919390100199.410.139860.137520.18552RANDOM26.231
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]
0.230.110.23-0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.904
r_sphericity_free23.813
r_sphericity_bonded11.55
r_dihedral_angle_4_deg10.645
r_dihedral_angle_3_deg9.849
r_rigid_bond_restr7.25
r_dihedral_angle_1_deg6.238
r_long_range_B_refined4.986
r_scangle_other4.935
r_long_range_B_other4.805
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.904
r_sphericity_free23.813
r_sphericity_bonded11.55
r_dihedral_angle_4_deg10.645
r_dihedral_angle_3_deg9.849
r_rigid_bond_restr7.25
r_dihedral_angle_1_deg6.238
r_long_range_B_refined4.986
r_scangle_other4.935
r_long_range_B_other4.805
r_scbond_it4.328
r_scbond_other4.328
r_mcangle_it3.584
r_mcangle_other3.582
r_mcbond_other3.077
r_mcbond_it3.076
r_angle_refined_deg2.556
r_angle_other_deg1.353
r_chiral_restr0.183
r_bond_refined_d0.031
r_gen_planes_refined0.014
r_gen_planes_other0.007
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 Atoms761
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms6

Software

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