5G4B

Crystal structure of Aura virus capsid protein in complex with piperazine.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AGK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.1 M BIS-TRIS AND 22 % POLYETHYLENE GLYCOL MONOMETHYL ETHER 2000, pH 6.5
Crystal Properties
Matthews coefficientSolvent content
1.9537.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.256α = 90
b = 34.839β = 101.94
c = 49.169γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMIRROR2013-10-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR-H

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
12.215079.60.0614.82.748472
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)
12.212.2541.60.2621.8

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 REPLACEMENTTHROUGHOUT4AGK2.2448.11461423274.290.201270.198640.26484RANDOM38.281
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]
-0.23-3.091.61-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.712
r_dihedral_angle_3_deg13.679
r_dihedral_angle_4_deg13.243
r_dihedral_angle_1_deg5.8
r_mcangle_it1.647
r_angle_refined_deg0.936
r_mcbond_it0.894
r_scbond_it0.691
r_chiral_restr0.06
r_bond_refined_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.712
r_dihedral_angle_3_deg13.679
r_dihedral_angle_4_deg13.243
r_dihedral_angle_1_deg5.8
r_mcangle_it1.647
r_angle_refined_deg0.936
r_mcbond_it0.894
r_scbond_it0.691
r_chiral_restr0.06
r_bond_refined_d0.004
r_gen_planes_refined0.004
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_it
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 Atoms1152
Nucleic Acid Atoms
Solvent Atoms65
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing