4Z4X

Crystal Structure of Multidrug Resistant HIV-1 Protease Clinical Isolate PR20D25N with Open Flap


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AOI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.92980.2M magnesium chloride and 20% PEG 3350.
Crystal Properties
Matthews coefficientSolvent content
2.4850.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.522α = 90
b = 45.522β = 90
c = 104.148γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2011-10-28MSINGLE 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
11.7541.7197.30.06517.93.8214442
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)
11.751.8198.60.4144.53.7

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 REPLACEMENTTHROUGHOUT2AOI1.7541.7119784106997.280.185990.184340.21687RANDOM19.826
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]
-0.09-0.090.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.077
r_dihedral_angle_4_deg21.919
r_dihedral_angle_3_deg12.524
r_dihedral_angle_1_deg7.474
r_long_range_B_refined5.066
r_long_range_B_other5.031
r_scangle_other3.877
r_scbond_it2.514
r_scbond_other2.514
r_angle_refined_deg2.506
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.077
r_dihedral_angle_4_deg21.919
r_dihedral_angle_3_deg12.524
r_dihedral_angle_1_deg7.474
r_long_range_B_refined5.066
r_long_range_B_other5.031
r_scangle_other3.877
r_scbond_it2.514
r_scbond_other2.514
r_angle_refined_deg2.506
r_mcangle_other2.159
r_mcangle_it2.156
r_mcbond_it1.453
r_mcbond_other1.442
r_angle_other_deg1.248
r_chiral_restr0.187
r_bond_refined_d0.031
r_gen_planes_refined0.015
r_gen_planes_other0.004
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 Atoms1518
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing
HKL-2000data scaling
SERGUIdata collection
HKL-2000data reduction