6O57

Crystal Structure of multi-drug resistant HIV-1 protease PR-S17 with a substrate analog p2-NC in P41


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.629829.5% PEG 4000, 0.2M ammonium acetate and 0.1M sodium acetate buffer at pH 4.6
Crystal Properties
Matthews coefficientSolvent content
2.8757.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.881α = 90
b = 54.881β = 90
c = 82.131γ = 90
Symmetry
Space GroupP 41

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-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
11.715099.10.0710.03121.26.12611737
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)
11.711.7795.20.4710.280.8172.63.4

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-VALUE1SGU1.7127.4624824126298.980.199840.19830.231RANDOM40.735
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]
0.710.71-1.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.418
r_dihedral_angle_3_deg14.326
r_dihedral_angle_4_deg9.79
r_dihedral_angle_1_deg7.924
r_long_range_B_refined6.822
r_long_range_B_other6.805
r_scangle_other5.87
r_mcangle_it4.1
r_mcangle_other4.098
r_scbond_other3.978
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.418
r_dihedral_angle_3_deg14.326
r_dihedral_angle_4_deg9.79
r_dihedral_angle_1_deg7.924
r_long_range_B_refined6.822
r_long_range_B_other6.805
r_scangle_other5.87
r_mcangle_it4.1
r_mcangle_other4.098
r_scbond_other3.978
r_scbond_it3.966
r_mcbond_it3.124
r_mcbond_other3.122
r_angle_refined_deg2.206
r_angle_other_deg1.171
r_chiral_restr0.141
r_bond_refined_d0.021
r_gen_planes_refined0.013
r_gen_planes_other0.005
r_bond_other_d0.001
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 Atoms78
Heterogen Atoms66

Software

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