6O5A

Crystal Structure of multi-drug resistant HIV-1 protease PR-S17 with a substrate analog p2-NC in P61


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SGU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729835% TacsimateTM, pH 7.0 (Hampton Research Corp., Aliso Viejo, CA). Tacsimate contains 1.83 M malonic acid, 0.25 M ammonium citrate tribasic, 0.12 M succinic acid, 0.3 M DL-malic acid, 0.4 M sodium acetate trihydrate, 0.5 M sodium formate, and 0.16 M ammonium tartrate dibasic.
Crystal Properties
Matthews coefficientSolvent content
2.2645.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.833α = 90
b = 63.833β = 90
c = 83.039γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2016-02-28MSINGLE 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)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
11.675098.40.0570.02916.94.42194528.6
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)
11.671.7389.20.4440.340.64122.3

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-VALUE1SGU1.6733.2220830107698.410.177530.175540.21617RANDOM31.165
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]
0.160.080.16-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.6
r_dihedral_angle_3_deg15.622
r_dihedral_angle_4_deg12.97
r_dihedral_angle_1_deg6.638
r_long_range_B_refined6.082
r_long_range_B_other6.064
r_scangle_other5.2
r_scbond_it3.314
r_scbond_other3.313
r_mcangle_it2.901
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.6
r_dihedral_angle_3_deg15.622
r_dihedral_angle_4_deg12.97
r_dihedral_angle_1_deg6.638
r_long_range_B_refined6.082
r_long_range_B_other6.064
r_scangle_other5.2
r_scbond_it3.314
r_scbond_other3.313
r_mcangle_it2.901
r_mcangle_other2.9
r_angle_refined_deg2.238
r_mcbond_it2.099
r_mcbond_other2.099
r_angle_other_deg1.124
r_chiral_restr0.125
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_gen_planes_other0.003
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1522
Nucleic Acid Atoms
Solvent Atoms125
Heterogen Atoms60

Software

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