2XDE

Crystal structure of the complex of PF-3450074 with an engineered HIV capsid N terminal domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
182ULOF PROTEIN (30MG/ML)AND 2UL OF WELL SOLUTION (20% PEG 8000, 100 MM PHOSPHATE-CITRATE PH 4.2 AND 200 MM SODIUM CHLORIDE
Crystal Properties
Matthew coefficientSolvent content
1.831.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.756α = 90
b = 71.035β = 90.41
c = 41.419γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2006-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
11.43098.80.063.4447352
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)
11.41.4899.40.063.4

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 REPLACEMENTTHROUGHOUTTRUNCATED MODEL OF N TERMINAL CAPSID1.420.72447021000.195460.195460.254RANDOM21.093
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]
-0.960.24-0.051.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.521
r_dihedral_angle_4_deg24.738
r_dihedral_angle_3_deg14.061
r_dihedral_angle_1_deg6.237
r_scangle_it3.748
r_scbond_it2.232
r_angle_refined_deg1.385
r_mcangle_it1.368
r_mcbond_it0.846
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.521
r_dihedral_angle_4_deg24.738
r_dihedral_angle_3_deg14.061
r_dihedral_angle_1_deg6.237
r_scangle_it3.748
r_scbond_it2.232
r_angle_refined_deg1.385
r_mcangle_it1.368
r_mcbond_it0.846
r_nbtor_refined0.314
r_nbd_refined0.234
r_symmetry_vdw_refined0.219
r_symmetry_hbond_refined0.18
r_xyhbond_nbd_refined0.165
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_gen_planes_other
r_metal_ion_other
r_bond_other_d
r_symmetry_vdw_other
r_nbtor_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_other
r_mcbond_other
r_metal_ion_refined
r_mcangle_other
r_xyhbond_nbd_other
r_scbond_other
r_angle_other_deg
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2124
Nucleic Acid Atoms
Solvent Atoms382
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing