4YE3

Crystal Structure of Multidrug Resistant HIV-1 Protease Clinical Isolate PR20 with Inhibitor GRL-4410A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52981.2M Sodium Chloride, 0.1M Sodium Acetate pH 5.5, 0.01M Yittrium Chloride
Crystal Properties
Matthews coefficientSolvent content
2.0941.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.349α = 90
b = 60.349β = 90
c = 85.775γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2013-10-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.8APS22-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
11.355099.10.06524.55.938558
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.492.40.4722.33.2

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 REPLACEMENTTHROUGHOUT3UCB1.35503855819281000.159380.157250.20019RANDOM19.96
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]
0.060.030.06-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.082
r_dihedral_angle_4_deg17.546
r_dihedral_angle_3_deg16.761
r_scangle_it8.477
r_dihedral_angle_1_deg7.65
r_scbond_it6.03
r_mcangle_it4.342
r_rigid_bond_restr3.195
r_mcbond_it2.94
r_angle_refined_deg2.698
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.082
r_dihedral_angle_4_deg17.546
r_dihedral_angle_3_deg16.761
r_scangle_it8.477
r_dihedral_angle_1_deg7.65
r_scbond_it6.03
r_mcangle_it4.342
r_rigid_bond_restr3.195
r_mcbond_it2.94
r_angle_refined_deg2.698
r_chiral_restr0.165
r_bond_refined_d0.029
r_gen_planes_refined0.016
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1518
Nucleic Acid Atoms
Solvent Atoms176
Heterogen Atoms62

Software

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