6O54

Crystal Structure of multi-drug resistant HIV-1 protease PR-S17 (D25N)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5T2E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52981.95 M sodium chloride, 0.1 M Bis-Tris, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.8656.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.645α = 90
b = 49.645β = 90
c = 86.703γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2017-02-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.215091.90.0710.03518.753545914.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.211.2552.10.4250.3180.75122.1

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 REPLACEMENTFREE R-VALUE5T2E1.2138.5533739170191.960.148540.147760.16411Random20.01
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]
-0.01-0.01-0.010.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.451
r_dihedral_angle_4_deg10.584
r_dihedral_angle_3_deg9.669
r_dihedral_angle_1_deg6.704
r_rigid_bond_restr6.647
r_long_range_B_refined6.253
r_long_range_B_other6.207
r_mcangle_it5.73
r_mcangle_other5.725
r_scangle_other4.768
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.451
r_dihedral_angle_4_deg10.584
r_dihedral_angle_3_deg9.669
r_dihedral_angle_1_deg6.704
r_rigid_bond_restr6.647
r_long_range_B_refined6.253
r_long_range_B_other6.207
r_mcangle_it5.73
r_mcangle_other5.725
r_scangle_other4.768
r_scbond_it4.556
r_scbond_other4.556
r_mcbond_other4.437
r_mcbond_it4.432
r_angle_refined_deg2.007
r_angle_other_deg1.434
r_chiral_restr0.121
r_bond_refined_d0.02
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.002
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
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms761
Nucleic Acid Atoms
Solvent Atoms105
Heterogen Atoms4

Software

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