5DCK

Crystal Structure of FIV Capsid C-Terminal Domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.22930.056M Sodium phosphate monobasic monohydrate, 1.344M Pottasium phosphate dibasic
Crystal Properties
Matthews coefficientSolvent content
3.2462.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.19α = 90
b = 64.19β = 90
c = 178.56γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTC2014-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-X1.54178

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
12.2940.6399.710.10817.9116.310456
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)
12.292.37296.960.5292.926.4

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 REPLACEMENTTHROUGHOUT3DTJ2.2940.63994650499.610.237770.235290.28683RANDOM41.833
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]
-17.21-17.2134.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.104
r_dihedral_angle_4_deg17.135
r_dihedral_angle_3_deg14.936
r_long_range_B_refined10.006
r_long_range_B_other9.981
r_dihedral_angle_1_deg6.708
r_scangle_other6.019
r_mcangle_it6.001
r_mcangle_other5.997
r_scbond_it3.981
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.104
r_dihedral_angle_4_deg17.135
r_dihedral_angle_3_deg14.936
r_long_range_B_refined10.006
r_long_range_B_other9.981
r_dihedral_angle_1_deg6.708
r_scangle_other6.019
r_mcangle_it6.001
r_mcangle_other5.997
r_scbond_it3.981
r_scbond_other3.962
r_mcbond_it3.872
r_mcbond_other3.844
r_angle_refined_deg1.515
r_angle_other_deg1.061
r_chiral_restr0.087
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.005
r_gen_planes_other0.005
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 Atoms1141
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing